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A Catalog of Published Genome-Wide Association Studies

Potential etiologic and functional implications of genome-wide association loci for human diseases and traitsPDF file
Click here to read our recent Proceedings of the Academy of Sciences (PNAS) article on catalog methods and analysis.

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Published Genome-Wide Associations
Credit: Darryl Leja and Teri Manolio

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The genome-wide association study (GWAS) publications listed here include only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage. Publications are organized from most to least recent date of publication, indexing from online publication if available. Studies focusing only on candidate genes are excluded from this catalog. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator).

SNP-trait associations listed here are limited to those with p-values < 1.0 x 10-5 (see full methods for additional details). Multipliers of powers of 10 in p-values are rounded to the nearest single digit; odds ratios and allele frequencies are rounded to two decimals. Standard errors are converted to 95 percent confidence intervals where applicable. Allele frequencies, p-values, and odds ratios derived from the largest sample size, typically a combined analysis (initial plus replication studies), are recorded below if reported; otherwise statistics from the initial study sample are recorded. For quantitative traits, information on % variance explained, SD increment, or unit difference is reported where available. Odds ratios < 1 in the original paper are converted to OR > 1 for the alternate allele. Where results from multiple genetic models are available, we prioritized effect sizes (OR's or beta-coefficients) as follows: 1) genotypic model, per-allele estimate; 2) genotypic model, heterozygote estimate, 3) allelic model, allelic estimate.

Gene regions corresponding to SNPs were identified from the UCSC Genome Browser. Gene names and risk alleles are those reported by the authors in the original paper. Only one SNP within a gene or region of high linkage disequilibrium is recorded unless there was evidence of independent association.

Occasionally the term "pending" is used to denote one or more studies that we identified as an eligible GWAS, but for which SNP information has not yet been extracted; studies of CNVs are also noted as pending.

How to cite the GWAS Catalog:
Hindorff LA, Junkins HA, Hall PN, Mehta JP, and Manolio TA. A Catalog of Published Genome-Wide Association Studies. Available at: www.genome.gov/gwastudies. Accessed [date of access].

How to cite the GWAS Catalog paper:
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, and Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA. [May 27, 2009.]

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As of 07/16/10, this table includes 607 publications and 2991 SNPs.
Date Added to Catalog (since 11/25/08) First Author/Date/ Journal/Study Disease/Trait Initial
Sample Size		 Replication Sample Size Region Reported Gene(s) Strongest SNP-Risk Allele Risk Allele Frequency in Controls P-value OR or beta-coefficient and [95% CI] Platform
[SNPs passing QC]		 CNV
07/14/10 Nischwitz
June 30, 2010
J Neuroimmunol
Evidence for VAV2 and ZNF433 as susceptibility genes for multiple sclerosis 		Multiple sclerosis 590 Caucasian European descent cases, 825 Caucasian European descent controls NR 6p21.32
10q11.21
19p13.2
9q34.2		 DQA1
Intergenic
ZNF433
VAV2		 rs9271366-G
rs2503875-A
rs3745672-?
rs3780792-G		 NR
NR
NR
NR		 4 x 10-17
2 x 10-7
1 x 10-6
1 x 10-6 		2.62 [2.09-3.28]
1.66 [1.37-2.00]
7.39 [3.32-16.47]
1.6 [1.32-1.92]		 Illumina
[~300,000]		 N
07/13/10 Dick
June 27, 2010
Mol Psychiatry
Genome-wide association study of conduct disorder symptomatology 		Conduct disorder (case status) 872 cases, 3,091 controls NR 4p15.32
2q21.2
11q14.3
10q11.22
10q26.11
13q31.1
4q31.21
2p11.2
4q31.21
8p22
2p24.3
4p15.32		 C1QTNF7
Intergenic
Intergenic
ARHGAP22
Intergenic
Intergenic
Intergenic
Intergenic
ZNF330
Intergenic
NAG
KIAA1345		 rs1861046-?
rs16831128-?
rs7950811-?
rs10776612-?
rs2184898-?
rs11838918-?
rs1550057-?
rs13398848-?
rs17007017-?
rs2720508-?
rs7581919-?
rs1861050-?		 0.095
0.189
0.071
0.519
0.327
0.022
0.757
0.074
0.685
0.907
0.041
0.063		 6 x 10-8
4 x 10-7
9 x 10-7
2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
7 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6 		1.65 [1.38-1.98]
1.45 [1.26-1.67]
1.65 [1.35-2.00]
1.33 [1.18-1.49]
1.33 [1.18-1.50]
2.26 [1.61-3.18]
1.39 [1.21-1.61]
1.59 [1.30-1.95]
1.34 [1.18-1.52]
1.61 [1.31-1.97]
1.85 [1.41-2.43]
1.63 [1.31-2.01]		 Illumina
[948,658]		 N
07/13/10 " Conduct disorder (symptom count) 872 cases, 3,091 controls NR 4p15.32
11q14.3
13q31.1
6q27
12q24.11
5q34
14q23.3
2q21.2
16p13.12
20q13.12
2p22.3
12p13.32
1q21.3
17p12		 C1QTNF7
Intergenic
Intergenic
PDE10A
SELPLG
Intergenic
Intergenic
Intergenic
ERCC4
TOX2
Intergenic
Intergenic
LOC343052
Intergenic		 rs16891867-?
rs7950811-?
rs11838918-?
rs7762160-?
rs8179116-?
rs2122554-?
rs1256531-?
rs16831128-?
rs3136202-?
rs6031252-?
rs6750486-?
rs12302829-?
rs4434872-?
rs4792394-?		 0.097
0.071
0.022
0.365
0.021
0.162
0.234
0.189
0.429
0.142
0.126
0.008
0.263
0.469		 3 x 10-9
1 x 10-8
1 x 10-8
1 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6 		.15 [NR] unit increase
.16 [NR] unit increase
.28 [NR] unit increase
.07 [NR] unit increase
.23 [NR] unit increase
.1 [NR] unit decrease
.09 [NR] unit increase
.08 [NR] unit increase
.07 [NR] unit decrease
.11 [NR] unit decrease
.1 [NR] unit increase
.35 [NR] unit decrease
.08 [NR] unit increase
.06 [NR] unit decrease		 Illumina
[948,658]		 N
07/12/10 Voight
June 27, 2010
Nat Genet
Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis 		Type 2 diabetes 8,130 European descent cases, 38,987 European descent controls Up to 34,412 European descent cases, 59,925 European descent controls 10q25.2
11q13.4
6p22.3
2q36.3
10q23.33
2p16.1
11q14.3
11p15.5
5q13.3
9p21.3
15q26.1
7q32.3
Xq26
8q22.1
15q25.1
3q27.2
7p15.1
12q14.3
8q24.11
12q24.31
16q12.2
4p16.1
9q21.31
3p25.2
17q12
12q21.1		 TCF7L2
CENTD2
CDKAL1
IRS1
HHEX,IDE
BCL11A
MTNR1B
KCNQ1
ZBED3
CDKN2A,CDKN2B
PRC1
KLF14
DUSP9
TP53INP1
ZFAND6
IGF2BP2
JAZF1
HMGA2
SLC30A8
HNF1A
FTO
WFS1
CHCHD9
PPARG
HNF1B,TCF2
TSPAN8,LGR5		 rs7903146-T
rs1552224-A
rs10440833-A
rs7578326-A
rs5015480-C
rs243021-A
rs1387153-T
rs231362-G
rs4457053-G
rs10965250-G
rs8042680-A
rs972283-G
rs5945326-G
rs896854-T
rs11634397-G
rs1470579-C
rs849134-A
rs1531343-C
rs3802177-G
rs7957197-T
rs11642841-A
rs1801214-T
rs13292136-C
rs13081389-A
rs4430796-G
rs4760790-A
2 x 10-51
1 x 10-22
2 x 10-22
5 x 10-20
1 x 10-15
3 x 10-15
8 x 10-15
3 x 10-13
3 x 10-12
1 x 10-10
2 x 10-10
2 x 10-10
3 x 10-10
1 x 10-9
2 x 10-9
2 x 10-9
3 x 10-9
4 x 10-9
1 x 10-8
2 x 10-8
3 x 10-8
3 x 10-8
3 x 10-8
2 x 10-7
2 x 10-6
4 x 10-6 		1.4 [1.34-1.46]
1.14 [1.11-1.17]
1.25 [1.20-1.31]
1.11 [1.08-1.13]
1.18 [1.13-1.23]
1.08 [1.06-1.10]
1.09 [1.06-1.11]
1.08 [1.06-1.10]
1.08 [1.06-1.11]
1.2 [1.13-1.27]
1.07 [1.05-1.09]
1.07 [1.05-1.10]
1.27 [1.18-1.37]
1.06 [1.04-1.09]
1.06 [1.04-1.08]
1.14 [1.09-1.19]
1.13 [1.09-1.18]
1.1 [1.07-1.14]
1.15 [1.10-1.21]
1.07 [1.05-1.10]
1.13 [1.08-1.18]
1.13 [1.08-1.18]
1.11 [1.07-1.15]
1.24 [1.15-1.35]
1.14 [1.08-1.20]
1.11 [1.06-1.16]		 Affymetrix & Illumina
[2,426,886] (imputed)		 N
07/16/10 Eriksson
June 24, 2010
PLoS Genet
Web-based, participant-driven studies yield novel genetic associations for common traits 		Common traits (Other) 9,126 Northern European ancestry individuals NR 1q21.3
1q44
2q35
2q22.3
1q21.3
2q24.3
10p12.2
14q24.3
9p24.1
15q26.1
6p21.33
9q34.11
11q22.3
21q22.3
2q24.2
8q24.22		 TCHH
OR2M7
WNT10A
Intergenic
LCE3E
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 rs17646946-A
rs4481887-G
rs7349332-T
rs10427255-C
rs499697-G
rs776488-?
rs11013962-?
rs2239557-?
rs1535480-?
rs7178909-?
rs6903896-?
rs7866070-?
rs10431058-?
rs425215-?
rs2270447-?
rs2014357-?		 0.20
0.74
0.14
0.46
0.29
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-42 (hair curl)
7 x 10-24 (asparagus anosmia)
3 x 10-14 (hair curl)
1 x 10-11 (sneeze)
1 x 10-10 (hair curl)
2 x 10-7 (footedness)
3 x 10-7 (earlobes)
3 x 10-7 (morningness)
4 x 10-7 (braces)
5 x 10-7 (optimism)
6 x 10-7 (sneeze)
7 x 10-7 (astigmatism)
8 x 10-7 (optimism)
8 x 10-7 (optimism)
8 x 10-7 (earlobes)
9 x 10-7 (sweet tooth)		 .29 [NR] unit decrease
1.67 [NR]
.19 [NR] unit increase
1.32 [NR]
.13 [NR] unit increase
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[535,076]		 N
07/16/10 " Eye color 9,126 Northern European ancestry individuals NR 15q13.1
15q13.1
14q32.12
14q32.12
11q14.3
6p25.3
5p13.2
11q14.3		 OCA2
OCA2
SLC24A4
SLC24A4
TYR
IRF4
SLC45A2
TYR		 rs12913832-A
rs12913832-A
rs12896399-G
rs12896399-T
rs1847134-A
rs12203592-T
rs16891982-C
rs1393350-A		 0.23
0.23
0.44
0.44
0.68
0.18
0.03
0.27		 1 x 10-300 (eye color)
3 x 10-52 (green eyes)
2 x 10-23 (green eyes)
1 x 10-16 (eye color)
1 x 10-15 (green eyes)
2 x 10-15 (eye color)
1 x 10-12 (eye color)
3 x 10-9 (eye color)		 2.49 [NR] unit increase
8.43 [NR]
1.73 [NR]
.34 [NR] unit decrease
1.58 [NR]
.42 [NR] unit decrease
.84 [NR] unit increase
.28 [NR] unit decrease		 Illumina
[535,076]		 N
07/16/10 " Freckling 9,126 Northern European ancestry individuals NR 6p25.3
16q24.3
20q11.22
9p22.2		 IRF4
MC1R
ASIP
BNC2		 rs12203592-T
rs12931267-G
rs619865-A
rs2153271-C		 0.18
0.08
0.10
0.41		 2 x 10-91
8 x 10-62
5 x 10-14
4 x 10-10 		1.61 [NR] unit increase
1.88 [NR] unit increase
.77 [NR] unit increase
.4 [NR] unit decrease		 Illumina
[535,076]		 N
07/16/10 " Hair color 9,126 Northern European ancestry individuals NR 15q13.1
16q24.3
6p25.3
5p13.2
5p13.2
20q11.21
14q32.12
16q24.3
11q13.3
11q24.2
6p25.3
8q24.3		 OCA2
MC1R
IRF4
NR
SLC45A2
ASIP
SLC24A4
MC1R
NR
NR
NR
NR		 rs12913832-A
rs12931267-G
rs12203592-T
rs16891982-?
rs16891982-C
rs291671-G
rs12896399-T
rs12931267-G
rs3750965-?
rs4935969-?
rs12203592-?
rs13263959-?		 0.23
0.08
0.18
NR
0.03
0.10
0.44
0.08
NR
NR
NR
NR		 9 x 10-88 (hair color)
5 x 10-87 (red hair)
2 x 10-28 (hair color)
4 x 10-20 (hair color)
4 x 10-20 (hair color)
2 x 10-15 (red hair)
5 x 10-13 (hair color)
3 x 10-10 (hair color)
3 x 10-7 (hair color)
4 x 10-7 (hair color)
4 x 10-7 (red hair)
8 x 10-7 (hair color)		 .97 [NR] unit increase
.56 [NR] unit increase
.59 [NR] unit increase
NR
1.1 [NR] unit increase
.22 [NR] unit increase
.31 [NR] unit decrease
.56 [NR] unit decrease
NR
NR
NR
NR		 Illumina
[535,076]		 N
07/12/10 Long
June 24, 2010
PLoS Genet
Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium 		Breast cancer 2,073 Chinese cases, 2,084 Chinese controls 8,986 Chinese cases, 6,653 Chinese controls, 1,612 Japanese cases, 1,602 Japanese controls, 2,797 European American cases, 2,662 European American controls 16q12.1 TOX3 rs4784227-T 0.24 1 x 10-28 (all races combined) 1.24 [1.20-1.29] Affymetrix
[684,457]		 N
07/04/10 Beall
June 22, 2010
Proc Natl Acad Sci USA
Natural selection on EPAS1 (HIF2{alpha}) associated with low hemoglobin concentration in Tibetan highlanders 		Hemoglobin concentrations 35 Tibetans 161 Tibetans NS NS NS NS NS NS Illumina
[502,722]		 N
07/12/10 McGovern
June 22, 2010
Hum Mol Genet
Fucosyltransferase 2(FUT2) Non-Secretor Status is associated with Crohn's Disease 		Crohn's disease 896 Caucasian cases, 3,204 Caucasian controls 1,174 Northern European origin cases, 357 Northern European origin controls 16q12.1
19q13.33
6q27
5q33.3
5q31.1
1p31.3
2q37.1		 NOD2
FUT2
CCR6,FGFR10P,RNASE2
IL12B
IBD5
IL23R
ATG16L1		 rs2066847-?
rs504963-A
rs2301436-?
rs10045431-?
rs2188962-?
rs11465804-?
rs2241880-?		 NR
0.431
NR
NR
NR
NR
NR		 2 x 10-15
2 x 10-8
6 x 10-8
7 x 10-8
1 x 10-7
1 x 10-6
3 x 10-6 		1.62 [1.42-1.86]
NR
1.37 [1.22-1.53]
1.45 [1.27-1.64]
1.36 [1.21-1.52]
1.89 [1.47-2.44]
1.32 [1.18-1.47]		 Illumina
[304,825]		 N
07/12/10 Turnbull
June 13, 2010
Nat Genet
Variants near DMRT1, TERT and ATF7IP are associated with testicular germ cell cancer 		Testicular germ cell cancer 979 UK cases, 4,947 UK controls 664 UK cases, 3,456 UK controls 12q21.32
5p15.33
9p24.3
5p15.33
5q31.3
12p13.1		 KITLG
TERT, CLPTM1L
DMRT1
TERT
SPRY4
ATF7IP		 rs3782181-?
rs4635969-T
rs755383-T
rs2736100-T
rs4624820-?
rs2900333-C		 0.78
0.19
0.62
0.49
0.54
0.62		 2 x 10-26
1 x 10-23
1 x 10-23
8 x 10-15
1 x 10-14
6 x 10-10 		2.22 [1.89-2.56]
1.54 [1.33-1.79]
1.37 [1.21-1.55]
1.33 [1.18-1.50]
1.47 [1.33-1.64]
1.27 [1.12-1.44]		 Illumina
[298,782]		 N
07/04/10 Hsu
June 10, 2010
PLoS Genet
An Integration of Genome-Wide Association Study and Gene Expression Profiling to Prioritize the Discovery of Novel Susceptibility Loci for Osteoporosis-Related Traits 		Osteoporosis 2,038 Caucasian women, 1,531 Caucasian men 5,595 Caucasian women, 2,126 Caucasian men 8q24.12
1p13.2
2q11.2
18q11.2
2q37.1
11p12
18q22.2		 TNFRSF11B
RAP1A
TBC1D8
OSBPL1A
SPP2
LRRC4C
DOK6		 rs2062375-G
rs494453-C
rs2278729-A
rs7227401-T
rs12151790-A
rs12808199-G
rs17184557-A		 0.45
0.24
0.33
0.39
0.40
0.43
0.23		 3 x 10-11 (LS BMD, women)
4 x 10-8 (NW, men & women)
1 x 10-7 (NSA, men)
4 x 10-7 (NW, men)
5 x 10-7 (FN BMD, women)
9 x 10-7 (FN BMD, men)
9 x 10-7 (LS BMD, women)		 .14 [NR] g/cm2 increase
NR
.19 [NR] unit decrease
.17 [NR] cm increase
.4 [NR] g/cm2 increase
.21 [NR] g/cm2 decrease
.13 [NR] g/cm2 increase		 Affymetrix
[433,510]		 N
07/12/10 Ramdas
June 10, 2010
PLoS Genet
A genome-wide association study of optic disc parameters 		Optic disc parameters 7,360 Caucasian individuals 4,455 Caucasian individuals 10q21.3
1p22.1
16q12.1		 ATOH7,PBLD
CDC7,TGFBR3
SALL1		 rs1900004-T
rs1192415-G
rs1362756-C		 0.22
0.18
0.28		 3 x 10-35
3 x 10-28
5 x 10-9 		.07 [0.06-0.08] mm decrease
.06 [0.05-0.07] mm increase
.03 [0.02-0.04] mm increase		 Affymetrix and Illumina
[~2.5 million] (imputed)		 N
07/12/10 " Vertical cup-disc ratio 7,360 Caucasian individuals 4,455 Caucasian individuals 9p21.3
14q23.1
11q13.1
13q13.3
22q12.1
10q21.3
17q23.2
1p36.23
19p13.3		 CDKN2B
SIX1
SCYL1
DCLK1
CHEK2
ATOH7, PBLD
BCAS3
RERE
ARID3A		 rs1063192-G
rs10483727-T
rs17146964-G
rs1926320-C
rs1547014-T
rs1900004-T
rs8068952-G
rs12025126-C
rs2159128-G		 0.46
0.41
0.20
0.24
0.29
0.22
0.23
0.29
0.13		 4 x 10-15
1 x 10-11
4 x 10-9
1 x 10-8
1 x 10-8
2 x 10-8
3 x 10-8
6 x 10-8
3 x 10-7 		.01 [0.010-0.018] mm2 decrease
.01 [0.008-0.016] mm2 increase
.01 [0.01-0.02] mm2 decrease
.01 [0.010-0.014] mm2 increase
.01 [0.007-0.015] mm2 decrease
.01 [0.009-0.017] mm2 decrease
.01 [0.008-0.016] mm2 decrease
.01 [0.007-0.015] mm2 decrease
.02 [0.01-0.03] mm2 decrease		 Affymetrix and Illumina
[~2.5 million] (imputed)		 N
07/01/10 Wang
June 09, 2010
Lancet
Common genetic determinants of vitamin D insufficiency: a genome-wide association study. 		Vitamin D insufficiency 16,125 European descent individuals 17,871 European descent individuals 4q13.3
11q13.4
11p15.2		 GC
DHCR7,NADSYN1
CYP2R1		 rs2282679-?
rs12785878-?
rs10741657-?		 0.29
0.23
0.40		 2 x 10-109
2 x 10-27
3 x 10-20 		NR
NR
NR		 Affymetrix & Illumina
[up to 2,548,976] (imputed)		 N
07/01/10 Bostrom
June 08, 2010
Hum Genet
Candidate genes for non-diabetic ESRD in African Americans: a genome-wide association study using pooled DNA 		End-stage renal disease (non-diabetic) 464 African American cases, 478 African American controls 336 African American cases, 363 African American controls 22q12.3 MYH9 rs4821469-? 0.056 2 x 10-19 2.86 [2.27-3.57] Illumina
[~550,000] (pooled)		 N
06/23/10 Oedegaard
June 07, 2010
Genes Brain Behav
A Genome- wide Association Study of Bipolar Disorder and Co-morbid Migraine 		Migraine in bipolar disorder 755 European American bipolar individuals 455 Norwegian ADHD cases NS NS NS NS NS NS Affymetrix
[724,067]		 N
07/01/10 Teupser
June 07, 2010
Circ Cardiovasc Genet
Genetic Regulation of Serum Phytosterol Levels and Risk of Coronary Artery Disease 		Serum Phytosterol Levels 1,495 European descent individuals 2,917 European descent individuals 2p21
2p21
9q34.2		 ABCG8
ABCG8
ABO		 rs4245791-C
rs41360247-C
rs657152-T		 0.322
0.064
0.383		 2 x 10-50 (campesterol)
6 x 10-25 (campesterol)
9 x 10-13 (campesterol)		 12 [NR] % increase
14 [NR] % decrease
8 [NR] % increase		 Affymetrix
[374,370]		 N
06/22/10 Johnson
June 06, 2010
Nat Genet
Genome-wide meta-analyses identifies seven loci associated with platelet aggregation in response to agonists 		Platelet aggregation Up to 3,991 European ancestry individuals Up to 840 African American individuals 1q23.1
1q23.1
19q13.42
10q25.2
10q21.3
7q36.3
9p24.1
10q24.33
10p13
11p15.4
12q13.3
20p13
6p22.1
8p22
11p15.5		 PEAR1
PEAR1
GP6
ADRA2A
JMJD1C
SHH
PTPRD
NEURL
MST151
MRVI1
HSD17B6
PRNP
TRIM27
SGCZ
KCNQ1		 rs12566888-A
rs12566888-A
rs1671152-T
rs869244-A
rs2893923-T
rs6943029-A
rs7044355-G
rs7071247-T
rs525455-G
rs7940646-T
rs12367822-T
rs6052699-A
rs4947339-T
rs1903595-G
rs179429-A		 0.103
0.102
0.142
0.353
0.336
0.067
0.501
0.119
0.459
0.381
0.277
0.507
0.438
0.303
0.167		 5 x 10-19 (epinephrine)
4 x 10-16 (ADP)
8 x 10-14 (collagen)
3 x 10-12 (epinephrine)
5 x 10-8 (epinephrine)
8 x 10-8 (ADP)
1 x 10-7 (collagen)
2 x 10-7 (epinephrine)
7 x 10-7 (ADP)
1 x 10-6 (ADP)
1 x 10-6 (collagen)
2 x 10-6 (epinephrine)
2 x 10-6 (epinehprine)
5 x 10-6 (ephinephrine)
7 x 10-6 (ADP)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix & Illumina
[~2.33 million] (imputed)		 N
06/22/10 Quan
June 06, 2010
Nat Genet
Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC 		Vitiligo 1,117 Chinese Han cases, 1,429 Chinese Han controls 5,910 Chinese Han cases, 9,916 Chinese Han controls, 713 Chinese Uygur cases, 824 Chinese Uygur controls 6p21.33
6p21.33
6q27
10q22.3		 HLA-C,HLA-B
HLA
RNASET2, FGFR1OP, CCR6
ZMIZ1		 rs11966200-A
rs9468925-?
rs2236313-T
rs11593576-?		 0.06
0.617
0.38
0.805		 1 x 10-48
2 x 10-33
1 x 10-16
8 x 10-7 		1.9 [1.74-2.07]
1.35 [1.28-1.41]
1.2 [1.15-1.25]
1.14 [1.09-1.20]		 Illumina
[493,909]		 N
06/22/10 Kasperaviciute
June 03, 2010
Brain
Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study 		Partial epilepsies Up to 3,445 European ancestry cases, 6,935 European ancestry controls NR 6q14.1
16p13.3
4q13.1
9q21.33
3p24.3
9p23		 AL132875.2
ADCY9
LPHN3
AL354897.1,AL451132.1
ZNF385D
PTPRD		 rs346291-?
rs2601828-A
rs2172802-?
rs2841498-?
rs1490157-?
rs2475335-?		 0.634
0.222
NR
NR
0.739
NR		 3 x 10-7
1 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
9 x 10-6 		1.2 [1.12-1.30]
1.12 [1.12-1.31]
NR
NR
1.2 [1.11-1.32]
NR		 Illumina
[528,745]		 N
06/21/10 Lewis
June 01, 2010
Am J Psychiatry
Genome-Wide Association Study of Major Recurrent Depression in the U.K. Population 		Major depressive disorder 1,636 UK cases, 1,594 UK controls 926 German cases, 866 German controls, 492 Caucasian cases, 1,052 Caucasian controls 1q31.3
5q14.3
3q26.31
6q27		 LOC647167
VCAN
NLGN1
LOC728275		 rs606149-?
rs310501-?
rs13074924-?
rs4709845-?		 0.46
0.33
0.36
0.85		 3 x 10-6
7 x 10-6
9 x 10-6
9 x 10-6 		1.25 [NR]
1.16 [NR]
1.18 [NR]
1.21 [NR]		 Illumina
[471,747]		 N
06/18/10 Nielsen
June 01, 2010
Psychiatr Genet
Genome-wide association study identifies genes that may contribute to risk for developing heroin addiction 		Heroin addiction 200 Caucasian and 125 African American severe former addicts, 150 Caucasians and 100 African American controls NR NS NS NS NS NS NS Affymetrix
[up to 113,174] (pooled)		 N
06/14/10 Wu
June 01, 2010
Pharmacogenet Genomics
Genome-wide examination of genetic variants associated with response to platinum-based chemotherapy in patients with small-cell lung cancer 		Response to platinum-based chemotherapy in small-cell lung cancer 245 Chinese Han cases 183 Chinese Han cases NS NS NS NS NS NS Affymetrix
[265,996]		 N
06/14/10 Bei
May 30, 2010
Nat Genet
A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. 		Nasopharyngeal carcinoma 1,583 Southern Chinese descent cases, 972 Southern Chinese descent controls, 922 Singapore Chinese controls 3,507 Southern Chinese descent cases, 3,063 Southern Chinese descent controls, 284 Southern Chinese family trios 6p22.1
6p21.33
6p21.32
13q12.12
13q12.12
3q26.2
9p21.3		 HLA-A
HLA-B,HLA-C
HLA-DQ,HLA-DR
TNFRSF19
TNFRSF19
MDS1,EVI1
CDNK2A,CDKN2B		 rs2860580-?
rs2894207-?
rs28421666-?
rs9510787-G
rs1572072-?
rs6774494-?
rs1412829-?		 0.62
0.82
0.88
0.37
0.74
0.35
0.89		 5 x 10-67
3 x 10-33
2 x 10-18
2 x 10-9
1 x 10-8
1 x 10-8
5 x 10-7 		1.72 [1.61-1.82]
1.64 [1.52-1.75]
1.49 [1.37-1.64]
1.2 [1.10-1.30]
1.19 [1.11-1.27]
1.19 [1.12-1.27]
1.28 [1.18-1.41]		 Illumina
[464,328]		 N
06/14/10 Diergaarde
May 17, 2010
Pancreatology
Pooling-Based Genome-Wide Association Study Implicates Gamma-Glutamyltransferase 1 (GGT1) Gene in Pancreatic Carcinogenesis 		Pancreatic cancer 97 unrelated Caucasian cases, 93 Caucasian controls NR NS NS NS NS NS NS Affymetrix
[NR](pooled)		 N
06/14/10 Liu
May 16, 2010
PLoS Genet
Digital quantification of human eye color highlights genetic association of three new loci 		Eye color traits 5,951 Dutch individuals 2,261 UK twins, 1,282 Australian family members 15q13.1
17q25.3
21q22.13		 HERC2,OCA
NPLOC4,HGS
TTC3,DSCR9		 rs12913832-?
rs9894429-T
rs1003719-A		 NR
NR
NR		 1 x 10-300 (RS123 cohort)
9 x 10-14 (CHS1)
2 x 10-10 (CHS1)		 NR
.12 [NR] % increase
.1 [NR] % decrease		 Illumina
[2,543,887] (imputed)		 N
06/14/10 Lu
May 13, 2010
PLoS Genet
Common genetic variants near the Brittle Cornea Syndrome locus ZNF469 influence the blinding disease risk factor central corneal thickness 		Central corneal thickness 1,714 Australian twins and family members, 1,759 UK twins and family members, 249 Australian thin CCT individuals, 251 thin CCT individuals, 102 Australian individuals from extreme CCT quantiles NR 16q24.2
13q14.11		 ZNF469
FOXO1		 rs12447690-C
rs2721051-G		 NR
NR		 9 x 10-11
5 x 10-10 		.16 [0.10-0.22] unit increase
.24 [0.16-0.32] unit decrease		 Illumina
[~2.4 million] (pooled)		 N
06/14/10 Seshadri
May 12, 2010
JAMA
Genome-wide Analysis of Genetic Loci Associated with Alzheimer Disease 		Alzheimer's disease 8,935 white individuals with 973 incident cases, 2,033 white prevalent cases, 14,642 white controls 6,505 white cases, 13,532 white controls 19q13.32 APOE rs2075650-G 0.14 1 x 10-295 2.53 [2.41-2.66] Affymetrix and Illumina
[~2.5 million] (imputed)		 N
06/09/10 Garcia-Barcelo
May 11, 2010
Hum Mol Genet
Genome-wide association study identifies a susceptibility locus for biliary atresia on 10q24.2 		Biliary atresia 200 Chinese cases, 481 Chinese controls 124 Chinese cases, 90 Chinese controls 10q25.1
13q12.3
12q13.13		 XPNPEP1,ADD3
UBL3
HOXC13		 rs17095355-T
rs9314986-G
rs2120991-A		 0.409
0.044
0.134		 7 x 10-9
2 x 10-6
9 x 10-6 		1.77 [1.38-2.26]
2.95 [1.89-4.60]
2.14 [1.58-2.89]		 Affymetrix
[289,118]		 N
06/13/10 Kochi
May 09, 2010
Nat Genet
A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility 		Rheumatoid arthritis 2,303 Japanese cases, 3,380 Japanese controls 4,768 Japanese cases, 17,359 Japanese controls 6p21.32
6q27
2q32.3
6q23.3		 HLA-DRB1
CCR6
STAT4
OLIG3,TNFAIP3		 rs13192471-G
rs3093024-T
rs7574865-T
rs2230926-C		 0.22
0.46
0.33
0.07		 2 x 10-58
8 x 10-19
2 x 10-6
2 x 10-6 		1.97 [1.82-2.14]
1.19 [1.15-1.24]
1.17 [1.10-1.25]
1.31 [1.17-1.46]		 Illumina
[393,217]		 N
06/08/10 Sanna
May 09, 2010
Nat Genet
Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis 		Multiple sclerosis 882 Sardinian cases, 872 Sardinian controls 1,775 Sardinian cases, 2,005 Sardinian controls 6p21.32
3q13.11		 HLA-DRB,HLA-DQB1
CBLB		 rs2040406-G
rs9657904-T		 0.26
0.826		 1 x 10-20
2 x 10-10 		2.05 [NR]
1.4 [1.27-1.57]		 Affymetrix
[6,607,266] (imputed)		 N
06/13/10 Stahl
May 09, 2010
Nat Genet
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock 		Rheumatoid arthritis 5,539 European ancestry cases, 20,169 European ancestry controls 6,768 European ancestry cases, 8,806 European ancestry controls 6p21.32
1p13.2
4p15.2
2q11.2
6q23.3
10p15.1
5q11.2
6q27
7q32.1
9p13.3
2p14
20q13.12
2q33.2
5q21.1
3p14.3
14q24.3
9q33.2
2q32.3
1p34.3
4q27
2p16.1
17q12
10p15.1
15q23
1q24.2
2q11.2
1p36.32
21q22.3
12q24.12		 HLA-DRB1
PTPN22
RBPJ
AFF3
TNFAIP3
IL2RA
ANKRD55,IL6ST
CCR6
IRF5
CCL21
SPRED2
CD40
CTLA4
C5orf30
PXK
BATF
TRAF1,C5
STAT4
POU3F1
IL2,IL21
REL
IKZF3
PRKCQ
KIF3
CD247
AFF3
TNFRSF14
UBASH3A
SH2B3		 rs6910071-G
rs2476601-A
rs874040-C
rs11676922-T
rs6920220-A
rs706778-T
rs6859219-C
rs3093023-A
rs10488631-C
rs951005-A
rs934734-G
rs4810485-T
rs3087243-G
rs26232-C
rs13315591-C
rs7155603-G
rs3761847-G
rs7574865-T
rs12131057-G
rs13119723-A
rs13031237-T
rs2872507-A
rs4750316-G
rs17374222-A
rs840016-C
rs10865035-A
rs3890745-T
rs11203203-A
rs3184504-T		 0.22
0.10
0.30
0.46
0.22
0.40
0.79
0.43
0.11
0.84
0.49
0.25
0.56
0.68
0.09
0.19
0.43
0.22
0.76
0.15
0.36
0.47
0.81
0.49
0.58
0.47
0.68
0.37
0.51		 1 x 10-299
9 x 10-74
1 x 10-16
1 x 10-14
9 x 10-13
1 x 10-11
1 x 10-11
2 x 10-11
4 x 10-11
4 x 10-10
5 x 10-10
3 x 10-9
1 x 10-8
4 x 10-8
5 x 10-8
1 x 10-7
2 x 10-7
3 x 10-7
4 x 10-7
7 x 10-7
8 x 10-7
9 x 10-7
2 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
4 x 10-6
4 x 10-6
6 x 10-6 		2.88 [2.73-3.03]
1.94 [1.81-2.08]
1.14 [NR]
1.12 [NR]
1.22 [1.16-1.29]
1.14 [NR]
1.28 [NR]
1.13 [NR]
1.19 [NR]
1.19 [NR]
1.13 [NR]
1.18 [1.11-1.25]
1.15 [1.10-1.20]
1.14 [NR]
1.29 [NR]
1.16 [NR]
1.13 [1.08-1.18]
1.16 [1.10-1.23]
1.16 [NR]
1.12 [NR]
1.13 [1.07-1.18]
1.1 [NR]
1.15 [1.09-1.22]
1.13 [NR]
1.11 [NR]
1.12 [1.07-1.17]
1.12 [1.06-1.18]
1.11 [NR]
1.08 [NR]		 Affymetrix & Illumina
[~2,716,259] (imputed)		 N
06/02/10 Turnbull
May 09, 2010
Nat Genet
Genome-wide association study identifies five new breast cancer susceptibility loci 		Breast cancer 3,659 UK cases, 4,897 UK controls 12,576 European cases, 12,223 European controls 10q26.13
11q13.3
16q12.1
10q21.2
2q35
10q22.3
5q11.2
9p21.3
10p15.1
3p24.1
8q24.21
11p15.5
6q25.1		 FGFR2
MYEOV,CCND1,ORAOV1,FGF19,FGF4,FGF3
TOX3
ZNF365
Intergenic
ZMIZ1
MAP3K1
CDKN2A,CDKN2B
ANKRD16,FBXO18
SLC4A7
Intergenic
LSP1
ESR1,C6orf97		 rs2981579-A
rs614367-T
rs3803662-A
rs10995190-G
rs13387042-A
rs704010-A
rs889312-C
rs1011970-T
rs2380205-C
rs4973768-T
rs1562430-T
rs909116-T
rs3757318-A		 0.42
0.15
0.26
0.85
0.49
0.39
0.28
0.17
0.57
0.47
0.58
0.53
0.07		 4 x 10-31
3 x 10-15
3 x 10-15
5 x 10-15
2 x 10-10
4 x 10-9
5 x 10-9
3 x 10-8
5 x 10-7
6 x 10-7
6 x 10-7
7 x 10-7
3 x 10-6 		1.43 [1.35-1.53]
1.15 [1.10-1.20]
1.3 [1.22-1.39]
1.16 [1.10-1.22]
1.21 [1.14-1.29]
1.07 [1.03-1.11]
1.22 [1.14-1.30]
1.09 [1.04-1.14]
1.06 [1.02-1.10]
1.16 [1.10-1.24]
1.17 [1.10-1.25]
1.17 [1.10-1.24]
1.3 [1.17-1.46]		 Illumina
[582,886]		 N
06/08/10 Kramer
May 06, 2010
Neurobiol Aging
Alzheimer disease pathology in cognitively healthy elderly: A genome-wide study 		Alzheimer's disease 299 non-demented Caucasian indidivuals (low and heavy NFT burden) NR 7q22.1
8p23.1		 RELN
MSRA		 rs4298437-?
rs11782819-?		 NR
NR		 2 x 10-6
3 x 10-6 		NR
NR		 Illumina
[292,175]		 N
06/02/10 Djurovic
May 05, 2010
J Affect Disord
A genome-wide association study of bipolar disorder in Norwegian individuals, followed by replication in Icelandic sample 		Bipolar disorder 194 Norwegian bipolar cases, 230 Norwegian schizophrenic cases, 336 Norwegian controls 435 Icelandic bipolar cases, 10,258 Icelandic controls NS NS NS NS NS NS Affymetrix
[up to 620,390]		 N
06/02/10 Smith
May 05, 2010
Circ Cardiovasc Genet
The Association of Genome-Wide Variation with the Risk of Incident Heart Failure in Adults of European and African Ancestry: A Prospective Meta-Analysis from the CHARGE Consortium 		Heart failure 20,926 European ancestry participants, 2,895 African ancestry participants NR 15q22.31
12q14.1
13q22.2
9p22.2
12q12
12q21.33
11q24.2
12p11.22
2q14.3
8q21.13
9p21.2
19p13.3
3q26.1
1q41
7p15.2
10q23.31		 USP3
LRIG3
TBC1D4
SH3GL2
PRICKLE1
BTG1
RPUSD4
TMTC1
LOC339760
SNX16
MOBKL2B
GNA15
BCHE
LOC100129376
EVX1
CH25H		 rs10519210-?
rs11172782-?
rs548097-?
rs2210327-?
rs1520832-?
rs17019682-?
rs563519-?
rs2046383-?
rs13418717-?
rs6473383-?
rs10812610-?
rs11880198-?
rs1523288-?
rs11118620-?
rs13225783-?
rs11203032-?		 0.03
0.29
0.02
0.19
0.04
0.17
0.66
0.30
0.20
0.15
0.50
0.13
0.65
0.29
0.05
0.10		 1 x 10-8 (EA)
7 x 10-8 (AA)
6 x 10-7 (EA)
7 x 10-7 (AA)
1 x 10-6 (EA)
2 x 10-6 (AA)
3 x 10-6 (AA)
3 x 10-6 (AA)
3 x 10-6 (AA)
3 x 10-6 (EA)
5 x 10-6 (EA)
6 x 10-6 (EA)
6 x 10-6 (EA)
7 x 10-6 (EA)
7 x 10-6 (EA)
8 x 10-6 (EA)		 1.53 [1.05-2.24]
1.46 [1.03-2.09]
1.62 [1.00-2.63]
3.14 [0.99-10.00]
1.39 [0.99-1.95]
1.47 [0.98-2.22]
1.45 [0.97-2.17]
1.39 [0.97-1.97]
1.46 [0.97-2.20]
1.19 [0.99-1.44]
1.14 [0.99-1.31]
1.23 [0.98-1.54]
1.15 [0.98-1.35]
1.15 [0.98-1.35]
1.38 [0.96-1.99]
1.22 [0.97-1.53]		 Affymetrix & Illumina
[2,478,304] (imputed)		 N
05/31/10 Albagha
May 02, 2010
Nat Genet
Genome-wide association study identifies variants at CSF1, OPTN and TNFRSF11A as genetic risk factors for Paget's disease of bone 		Paget's disease 692 European ancestry cases, 1,001 European ancestry controls 481 European ancestry cases, 520 European ancestry controls 1p13.3
18q21.33
10p13
18q21.33		 CSF1
TNFRSF11A
OPTN
TNFRSF11A		 rs484959-?
rs3018362-A
rs1561570-?
rs2957128-A		 0.51
0.34
0.55
0.38		 5 x 10-24
5 x 10-13
6 x 10-13
2 x 10-11 		1.82 [1.61-2.04]
1.52 [1.36-1.70]
1.54 [1.37-1.72]
1.46 [1.30-1.63]		 Illumina
[294,663]		 N
05/26/10 Beaty
May 02, 2010
Nat Genet
A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4 		Cleft lip 825 European ancestry trios, 1,038 Asian ancestry trios 2,194 Asian family members, 322 South Asian family members, 3,830 European descent family members, 1,769 South/Central American family members 8q24.21
1q32.2		 MAFB
IRF6		 rs987525-A
rs10863790-?		 0.17
0.80		 4 x 10-16
1 x 10-14 		1.78 [1.55-2.05]
1.72 [1.49-1.98]		 Illumina
[589,945]		 N
05/26/10 Suchindran
April 29, 2010
PLoS Genet
Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study 		Lipoprotein-associated phospholipase A2 activity and mass 6,668 Caucasian individuals NR 19q13.32
1p13.3
6p12.3
12q24.31
11q23.3		 APOC1
PSRC1
PLA2G7
SCARB1
ZNF259		 rs4420638-G
rs599839-G
rs1805017-T
rs10846744-C
rs12286037-T		 0.16
0.22
0.26
0.15
0.07		 6 x 10-24 (activity)
3 x 10-15 (activity)
6 x 10-14 (mass)
1 x 10-8 (activity)
4 x 10-8 (activity)		 8 [NR] nmol/ml/min increase
5.5 [NR] nmol/ml/min decrease
11.1 [NR] ng/mL increase
4.6 [NR] nmol/ml/min increase
6.4 [NR] nmol/ml/min increase		 Affymetrix
[360,811]		 N
05/26/10 Hodgkinson
April 26, 2010
Proc Natl Acad Sci USA
Genome-wide association identifies candidate genes that influence the human electroencephalogram 		Electroencephalogram traits 322 Plains American Indian individuals 185 European Americans NS NS NS NS NS NS Illumina
[405,281]		 N
05/25/10 Levy
April 26, 2010
Proc Natl Acad Sci USA
Genome-wide association identifies OBFC1 as a locus involved in human leukocyte telomere biology 		Telomere length 3,417 European ancestry individuals 1,893 African American and white individuals, 2,876 British women 10q24.33
19p12
2q22.1
6p21.33		 OBFC1
ZNF676
CXCR4
SLC44A4		 rs4387287-A
rs1975174-T
rs4452212-A
rs2736428-T		 NR
NR
NR
NR		 2 x 10-11
2 x 10-6
2 x 10-6
3 x 10-6 		.1 [0.06-0.14] kb increase
.05 [0.03-0.07] kb increase
.05 [0.03-0.07] kb decrease
.05 [0.03-0.07] kb increase		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
05/24/10 Liu
April 25, 2010
Nat Genet
Meta-analysis and imputation refines the association of 15q25 with smoking quantity 		Smoking behavior 41,150 European descent individuals 120,516 European descent individuals 15q25.1 CHRNA5,CHRNA3 rs1051730-G 0.66 2 x 10-66 .08 [0.07-0.09] unit decrease Affymetrix & Illumina
[NR] (imputed)		 N
05/24/10 The Tobacco and Genetics Consortium
April 25, 2010
Nat Genet
Genome-wide meta-analyses identify multiple loci associated with smoking behavior 		Smoking behavior Up to 74,035 European ancestry individuals Up to 68,988 participants 15q25.1
10q23.32
19q13.2
11p14.1
9q34.2		 CHRNA3
LOC100188947
CYP2A6,EGLN2
BDNF
DBH		 rs1051730-G
rs1329650-T
rs3733829-G
rs6265-C
rs3025343-G		 0.65
0.28
0.36
0.79
0.84		 3 x 10-73 (CPD)
6 x 10-10 (CPD)
1 x 10-8 (CPD)
2 x 10-8 (smoking initiation)
4 x 10-8 (smoking cessation)		 1.02 [0.91-1.13] CPD decrease
.37 [0.25-0.49] CPD decrease
.33 [0.22-0.44] CPD increase
1.06 [1.04-1.08]
1.12 [1.08-1.18]		 Affymetrix, Illumina and Perlegen
[~2.5 million] (imputed)		 N
05/24/10 Thorgeirsson
April 25, 2010
Nat Genet
Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior 		Smoking behavior 31,266 European ancestry individuals 54,731 European descent individuals 15q25.1
19q13.2
8p11.21
7p14.3
19q13.2		 NR
CYP2A6,RAB4D
CHRNB3,CHRNA6
Intergenic
CYP2B6		 rs1051730-A
rs4105144-C
rs6474412-T
rs215614-G
rs7260329-G		 0.34
0.70
0.78
0.36
0.69		 2 x 10-69
2 x 10-12
1 x 10-8
2 x 10-7
6 x 10-6 		.8 [0.70-0.90] CPD increase
.39 [0.27-0.51] CPD increase
.29 [0.19-0.39] CPD increase
.22 [0.14-0.30] CPD increase
.2 [0.12-0.28] CPD increase		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
05/23/10 Ahn
April 23, 2010
Hum Mol Genet
Genome-wide association study of circulating vitamin D levels 		Vitamin D levels 4,501 European ancestry individuals 2,221 European ancestry individuals 4q13.3
11p15.2
11q13.4		 GC
CYP2R1
NADSYN1,DHCR7		 rs2282679-C
rs2060793-A
rs3829251-A		 0.26
0.41
0.19		 2 x 10-49
3 x 10-17
3 x 10-9 		.38 [0.32-0.44] unit decrease
.25 [0.15-0.35] unit increase
.18 [0.12-0.24] unit decrease		 Affymetrix & Illumina
[593,253] (imputed)		 N
05/23/10 Qi
April 23, 2010
Hum Mol Genet
Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes 		Type 2 diabetes 2,591 European ancestry cases, 3,052 European ancestry controls 10,870 European origin cases, 73,735 European origin controls 2q24.2 RBMS1, ITGB6 rs7593730-? 0.78 4 x 10-8 1.11 [1.08-1.16] Affymetrix
[683,509]		 N
05/20/10 Scherag
April 22, 2010
PLoS Genet
Two new loci for body-weight regulation identified in a joint analysis of genome-wide association studies for early-onset extreme obesity in French and German study groups 		Obesity (extreme) 1,138 French and German extremely obese children, 1,120 French and German normal or underweight children 1,892 European ancestry obese or overweight children and adolescents, 3,763 European ancestry normal or underweight controls, 715 families with obese offspring 16q12.2
18q21.32		 FTO
MC4R		 rs1558902-A
rs10871777-A		 NR
NR		 7 x 10-13
6 x 10-11 		1.37 [1.26-1.50]
1.22 [1.09-1.37]		 Affymetrix & Illumina
[1,596,878] (imputed)		 N
05/18/10 Jin
April 21, 2010
N Engl J Med
Variant of TYR and Autoimmunity Susceptibility Loci in Generalized Vitiligo 		Vitiligo 1,392 European ancestry cases, 2,629 European ancestry controls 647 European ancestry cases, 1,056 European ancestry controls, 183 European ancestry trios, 332 European ancestry multiplex families 6p22.1
6p21.32
11q14.3
22q12.3
1p36.23
3q28
21q22.3
10p15.1
14q12
1p13.2		 HLA-A,HCG9
BTNL2,HLA-DRA,HLA-DQA1
TYR
C1QTNF6
RERE
LPP
UBASH3A
IL2RA,RBM17,PFKB3
GZMB
PTPN22		 rs6904029-A
rs3806156-T
rs1393350-G
rs229527-T
rs4908760-G
rs1464510-T
rs11203203-A
rs706779-A
rs8192917-G
rs2476601-A		 0.29
0.37
0.733
0.419
0.37
0.44
0.373
0.535
0.236
0.095		 1 x 10-21
7 x 10-19
2 x 10-18
2 x 10-16
7 x 10-15
1 x 10-11
1 x 10-9
3 x 10-9
3 x 10-8
1 x 10-7 		1.49 [1.37-1.61]
1.42 [1.32-1.54]
1.53 [1.39-1.68]
1.38 [1.28-1.50]
1.36 [1.26-1.48]
1.31 [1.21-1.41]
1.27 [1.18-1.38]
1.27 [1.17-1.37]
1.28 [1.17-1.39]
1.39 [1.23-1.57]		 Illumina
[520,460]		 N
05/23/10 Morrison
April 17, 2010
Circ Cardiovasc Genet
Genomic Variation Associated with Mortality among Adults of European and African Ancestry with Heart Failure: The CHARGE Consortium 		Mortality among heart failure patients 2,526 European ancestry individuals, 466 African ancestry individuals NR 3p22.3
15q13.3
19p13.12
12q24.33
5p13.3
1q41
4q34.2
10q22.3
11p15.3
14q32.11
7q31.1		 CMTM7
OTUD7A
LPHN1
LOC338797
ADAMTS12
LOC400804
GPM6A
KCNMA1
PARVA
KCNK13
IFRD1		 rs12638540-G
rs2125623-C
rs4528684-T
rs7965445-A
rs6868223-A
rs12733856-A
rs7687921-T
rs4979906-G
rs7120489-A
rs8017423-T
rs17159640-T		 0.043
0.71
0.094
0.098
0.338
0.382
0.039
0.186
0.069
0.62
0.048		 3 x 10-7 (EA)
1 x 10-6 (EA)
1 x 10-6 (EA)
2 x 10-6 (EA)
2 x 10-6 (AA)
3 x 10-6 (AA)
4 x 10-6 (EA)
7 x 10-6 (EA)
7 x 10-6 (EA)
7 x 10-6 (AA)
9 x 10-6 (EA)		 1.53 [1.01-2.31]
1.23 [0.99-1.54]
1.42 [0.99-2.03]
1.3 [0.99-1.72]
1.58 [0.98-2.56]
1.56 [0.97-2.51]
1.77 [0.95-3.28]
1.23 [0.98-1.55]
1.35 [0.96-1.90]
1.64 [0.94-2.78]
1.59 [0.94-2.68]		 Affymetrix
[~2.4 million] (imputed)		 N
05/12/10 Kang
April 16, 2010
Hum Mol Genet
Genome wide association of anthropometric traits in African and African derived populations 		Anthropometric traits 743 African Americans, 1,188 Nigerians 756 African American family members, 982 African Americans, 2,437 Jamaicans NS NS NS NS NS NS Affymetrix
[~2.9] million (imputed)		 N
05/18/10 MacGregor
April 15, 2010
Hum Mol Genet
Genome-wide association identifies ATOH7 as a major gene determining human optic disc size 		Optic disc size (cup) 1,368 Australian twins, 848 UK individuals NR 10q21.3
3p25.1
4q12
7q34
11q13.4
12q21.33
1q41
5q33.1
8p23.1		 ATOH7
RFTN1
SCFD2
DENND2A
PDE2A
LOC643153
ESRRG
NMUR2
LOC401447		 rs3858145-A
rs690037-C
rs2898681-G
rs10237118-C
rs12418204-G
rs10858945-A
rs1436900-T
rs1010254-C
rs9692809-C		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7
2 x 10-7
2 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6 		.21 [0.12-0.30] unit increase
.21 [0.13-0.29] unit increase
.17 [0.07-0.27] unit increase
.31 [0.15-0.47] unit increase
.31 [0.10-0.51] unit increase
.17 [0.09-0.25] unit decrease
.14 [0.06-0.22] unit decrease
.18 [0.08-0.28] unit increase
.09 [-0.15-0.33] unit decrease		 Illumina
[~2.74 million] (imputed)		 N
05/18/10 " Optic disc size (disc) 1,368 Australian twins, 848 UK individuals NR 10q21.3
10q21.3
10q21.3
1p22.1
2q22.1
Xp11.23
14q32.2		 PBLD
ATOH7
MYPN
HSP90B3P
LRP1B
ZNF157
MEG3		 rs12571093-G
rs3858145-A
rs6480314-A
rs1192415-A
rs491391-A
rs6611365-G
rs1884537-C		 NR
NR
NR
NR
NR
NR
NR		 2 x 10-10
3 x 10-10
2 x 10-7
3 x 10-7
3 x 10-7
4 x 10-7
2 x 10-6 		.31 [0.20-0.42] unit increase
.3 [0.20-0.39] unit increase
.24 [0.13-0.35] unit increase
.25 [0.14-0.35] unit decrease
.41 [0.22-0.60] unit decrease
.18 [0.10-0.26] unit increase
.13 [0.05-0.21] unit increase		 Illumina
[~2.74 million] (imputed)		 N
05/18/10 " Optic disc size (rim) 1,368 Australian twins, 848 UK individuals NR 6q21
14q31.1
1p36.22
13q22.1
14q23.1
22q12.3		 hCG_1820801
TSHR
PEX14
LOC730245
SIX1
MYH9		 rs9488363-G
rs17111394-T
rs12741973-C
rs8000245-C
rs10483727-C
rs735854-C		 NR
NR
NR
NR
NR
NR		 2 x 10-6
4 x 10-6
7 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6 		.15 [0.07-0.23] unit decrease
.22 [0.11-0.33] unit increase
.17 [0.09-0.25] unit decrease
.21 [0.09-0.33] unit increase
.15 [0.06-0.24] unit increase
.16 [0.08-0.24] unit decrease		 Illumina
[~2.74 million] (imputed)		 N
05/10/10 Pelak
April 15, 2010
J Infect Dis
Host determinants of HIV-1 control in African Americans 		HIV-1 control 515 African American cases NR 20p12.3
6p21.33
7p14.2
19p13.2
11q14.1
13q31.3
3p24.3
6q22.31
8p21.3
8p21.3		 MCM8
HLA-B
AOAH
EVI5L
Intergenic
GPC5
AC023798.16
RP11-100A16.1
PPP3CC
SORBS3		 rs454422-?
rs2523608-?
rs6948404-?
rs558718-?
rs1357339-?
rs1413191-?
rs2593321-?
rs2789066-?
rs4872511-?
rs2280890-?		 0.26
0.37
0.07
0.11
0.04
0.18
0.23
0.13
0.01
0.01		 1 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[1,212,217]		 N
05/07/10 Lee
April 13, 2010
Mol Psychiatry
Genome-wide association study of bipolar I disorder in the Han Chinese population 		Bipolar disorder 1,000 Han Chinese cases, 1,000 Han Chinese controls 409 Han Chinese cases, 1,000 Han Chinese controls 7p21.1
15q26.1
13q22.3		 SP8
ST8SIA2,C15orf32
BTF3L1,KCTD12		 rs2709736-G
rs8040009-C
rs2073831-T		 NR
0.11
0.37		 5 x 10-7
6 x 10-6
1 x 10-5 		1.44 [1.25-1.66] (GG genotype)
1.4 [1.21-1.61]
1.33 [1.17-1.51]		 Illumina
[516,919]		 N
05/06/10 Chen
April 12, 2010
Proc Natl Acad Sci USA
Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration 		Age-related macular degeneration 2,978 European ancestry cases, 2,859 European ancestry controls 7,071 European ancestry cases, 678 Japanese cases, 4,289 European ancestry controls, 336 Japanese controls 1q31.3
10q26.13
6p21.33
1q31.3
22q12.3
19p13.3
6p21.33
15q21.3
4q25
16q13
12q13.3
18q21.32		 CFH
ARMS2,HTRA1
C2,CFB
CFH
TIMP3
C3
C2,CFB
LIPC
CFI
CETP
NR
NR		 rs10737680-A
rs3793917-G
rs429608-G
rs1329424-T
rs9621532-A
rs2230199-C
rs9380272-A
rs493258-C
rs2285714-T
rs3764261-A
rs2958154-C
rs11878133-T		 0.566
0.164
0.842
0.351
0.95
0.163
0.012
0.56
0.395
0.32
NR
NR		 2 x 10-76
4 x 10-60
3 x 10-21
6 x 10-16
1 x 10-11
1 x 10-10
2 x 10-8
1 x 10-7
3 x 10-7
7 x 10-7
2 x 10-6
4 x 10-6 		3.11 [2.76-3.51]
3.4 [2.94-3.94]
2.16 [1.84-2.53]
1.88 [1.68-2.10]
1.41 [1.27-1.57]
1.74 [1.47-2.06]
4.31 [2.76-6.87]
1.14 [1.09-1.20]
1.31 [1.18-1.45]
1.19 [1.12-1.27]
NR
NR		 Illumina
[~2.5 million] (imputed)		 N
05/06/10 Neale
April 12, 2010
Proc Natl Acad Sci USA
Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC) 		Age-related macular degeneration 979 European ancestry cases, 1,709 European ancestry controls 5,789 Caucasian cases, 4,234 Caucasian controls 10q26.13
1q31.3
1q31.3
6p21.33
22q12.3
4q25
15q21.3
15q21.3
19p13.3
6p24.3
3q12.1		 ARMS2,HTRA1
CFH
CFH
CFB,C2
TIMP3
CFI
LIPC
Intergenic
C3
RREB1
COL8A1		 rs10490924-?
rs1061170-?
rs1410996-?
rs641153-?
rs9621532-A
rs10033900-?
rs10468017-?
rs493258-C
rs2230199-?
rs11755724-G
rs13095226-C		 NR
NR
NR
NR
0.96
NR
0.70
0.55
NR
0.64
0.12		 5 x 10-119
4 x 10-117
2 x 10-111
2 x 10-20
4 x 10-9
9 x 10-9
1 x 10-8
2 x 10-8
2 x 10-8
1 x 10-6
3 x 10-6 		NR
NR
NR
NR
1.61 [1.37-1.89]
NR
1.22 [1.14-1.30]
1.16 [1.10-1.22]
NR
1.15 [1.09-1.14]
1.24 [1.13-1.35]		 Affymetrix
[632,932]		 N
05/05/10 Chambers
April 11, 2010
Nat Genet
Genetic loci influencing kidney function and chronic kidney disease 		Serum creatinine 23,812 European descent individuals 16,626 European individuals 2p13.1
19q13.11
17q23.2
6q25.3
4q21.1		 NAT8,NAT8B,ALMS1,DUSP11,TPRKB
SLC7A9
TBX2
SLC22A2
SHROOM3		 rs10206899-G
rs4805834-A
rs8068318-G
rs3127573-G
rs9992101-?		 0.22
0.13
0.27
0.13
NR		 1 x 10-15
5 x 10-11
3 x 10-10
7 x 10-10
6 x 10-9 		1 [0.7-1.2] % decrease
1 [0.7-1.3] % decrease
.8 [0.6-1.0] % increase
1.1 [0.8-1.4] % increase
NR		 Affymetrix, Illumina and Perlegen
[~2.6 Million] (imputed)		 N
05/05/10 Kottgen
April 11, 2010
Nat Genet
New loci associated with kidney function and chronic kidney disease 		Chronic kidney disease Up to 67,093 European ancestry individuals Up to 22,982 European ancestry individuals 20p11.21
15q21.1
16p12.3
4q21.1
15q24.2
17q23.2
2q34
19q13.11
5q35.3
2p23.3
2p13.1
9q21.11
6p21.1
15q21.3
1q21.3
7q36.1
6q25.3
13q21.33
3q23
12q24.12
12p13.33
7q11.23
10p15.3
8p21.2
11q13.1
1p13.3
5p13.1
2p25.2		 CST3,CST4,CST9
GATM, SPATA5L1
UMOD,ACSM5,GP2,PDILT
SHROOM3, CCDC158
UBE2Q2,FBX022
BCAS3,TBX2,C17orf82
CPS1
SLC7A9,CCDC123,ECAT8
SLC34A1,GRK6,RGS14,LMAN2,PRR7,F12,PFN3
GCKR, IFT172, FNDC4
NAT8,NAT8B,ALMS1
PIP5K1B,FAM122A
VEGFA
WDR72
ANXA9,FAM63A,PRUNE,BNIPL,LASS2,SETDB1
PRKAG2
SLC22A2
DACH1
TFDP2
ATXN2
SLC6A13, JARID1A, SLC6A12
TMEM60,RSBN1L, PHTF2
WDR37
STC1
RNASEH2C,KAT5,OVOL1
SYPL2,ATXN7L2,CYB561D1,PSMA5,AMIGO1,SORT1
DAB2,C9
SOX11		 rs911119-?
rs2453533-?
rs12917707-T
rs17319721-A
rs1394125-A
rs9895661-C
rs7422339-A
rs12460876-C
rs6420094-G
rs1260326-T
rs13538-G
rs4744712-A
rs881858-G
rs491567-C
rs267734-C
rs7805747-A
rs2279463-G
rs626277-C
rs347685-C
rs653178-T
rs10774021-C
rs6465825-C
rs10794720-T
rs10109414-T
rs4014195-G
rs1933182-A
rs11959928-A
rs16864170-C		 0.21
0.38
0.18
0.43
0.35
0.19
0.32
0.39
0.34
0.41
0.23
0.39
0.28
0.22
0.20
0.24
0.12
0.40
0.28
0.50
0.36
0.39
0.08
0.42
0.35
0.30
0.44
0.05		 2 x 10-138 (eGFRcys)
5 x 10-22 (eGFRcrea)
1 x 10-20 (eGFRcrea)
1 x 10-19 (eGFRcrea)
3 x 10-17 (eGFRcrea)
1 x 10-15 (eGFRcrea)
1 x 10-15 (eGFRcrea)
3 x 10-15 (eGFRcrea)
1 x 10-14 (eGFRcrea)
3 x 10-14 (eGFRcrea)
5 x 10-14 (eGFRcrea)
8 x 10-14 (eGFRcrea)
9 x 10-14 (eGFRcrea)
3 x 10-13 (eGFRcrea)
1 x 10-12 (eGFRcrea)
4 x 10-12 (CKD)
6 x 10-12 (eGFRcrea)
3 x 10-11 (eGFRcrea)
3 x 10-11 (eGFRcrea)
4 x 10-11 (eGFRcys)
1 x 10-9 (eGFRcrea)
2 x 10-9 (eGFRcrea)
1 x 10-8 (eGFRcrea)
1 x 10-8 (eGFRcrea)
1 x 10-7 (eGFRcrea)
1 x 10-7 (eGFRcrea)
1 x 10-7 (eGFRcrea)
2 x 10-7 (CKD)		 NR
NR
NR
NR
.01 [0.007-0.011] ml/min/1.73 m2 decrease
.01 [0.007-0.015] ml/min/1.73 m2 decrease
.01 [0.005-0.013] ml/min/1.73 m2 decrease
.01 [0.006-0.01] ml/min/1.73 m2 increase
.01 [0.007-0.015] ml/min/1.73 m2 decrease
.01 [0.007-0.011] ml/min/1.73 m2 increase
.01 [0.005-0.013] ml/min/1.73 m2 increase
.01 [0.008-0.016] ml/min/1.73 m2 decrease
1.08 [0.007-0.015] ml/min/1.73 m2 increase
.01 [0.005-0.013] ml/min/1.73 m2 increase
.01 [0.004-0.016] ml/min/1.73m2 increase
1.18 [1.12-1.25]
.01 [0.009-0.017] ml/min/1.73 m2 decrease
.01 [0.007-0.011] ml/min/1.73 m2 increase
1.09 [0.007-0.011] ml/min/1.73 m2 increase
.01 [0.009-0.017] ml/min/1.73 m2 increase
1.05 [0.006-0.010] ml/min/1.73 m2 increase
.01 [0.006-0.01] ml/min/1.73 m2 decrease]
.01 [0.010-0.018] ml/min/1.73 m2 decrease
NR
.01 [0.006-0.010] ml/min/1.73 m2 decrease
.01 [0.006-0.010] ml/min/1.73m2 decrease
.01 [0.007-0.011] ml/min/1.73 m2 decrease
1.3 [1.18-1.43]		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
05/03/10 Radstake
April 11, 2010
Nat Genet
Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus 		Systemic sclerosis 2,296 European ancestry cases, 5,171 European ancestry controls 2,753 European ancestry cases, 4,569 European ancestry controls 6p21.32
7q32.1
1q24.2
2q32.3		 HLADQB1
TNPO, IRF5
CD247
STAT4		 rs6457617-?
rs10488631-C
rs2056626-?
rs3821236-A		 0.53
NR
0.59
0.20		 4 x 10-17
2 x 10-13
3 x 10-9
3 x 10-9 		1.37 [1.28-1.47]
1.5 [1.35-1.67]
1.16 [1.11-1.23]
1.3 [1.19-1.41]		 Illumina
[279,621]		 N
04/27/10 Freathy
April 06, 2010
Nat Genet
Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight 		Birth weight 10,623 European descent individuals 27,591 European descent individuals 3q25.31
3q21.1		 CCNL1, LEKR1
ADCY5		 rs900400-C
rs9883204-C
2 x 10-35
7 x 10-15 		.09 [0.073-0.10] s.d. decrease
.06 [0.047-0.079] s.d. decrease		 Affymetrix & Illumina
[~2.4 million] (imputed)		 N
04/27/10 Ma
April 06, 2010
BMC Med Genet
Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham Heart Study data. 		Cholesterol 6,078 European descent individuals 1,231 Italian participants NS NS NS NS NS NS NR
[432,096]		 N
05/10/10 Yasuno
April 04, 2010
Nat Genet
Genome-wide association study of intracranial aneurysm identifies three new risk loci 		Intracranial aneurysm 2,780 European cases, 12,515 European controls 3,111 Japanese cases, 1,666 Japanese controls 9p21.3
18q11.2
8q11.23
10q24.32
13q13.1
8q11.23		 CDKN2A,CDKN2B
RBBP8
SOX17
CNNM2
STARD13
SOX17		 rs1333040-T
rs11661542-C
rs9298506-A
rs12413409-G
rs9315204-T
rs1504749-C		 0.56
0.49
0.81
0.91
0.21
0.21		 2 x 10-22
1 x 10-12
1 x 10-12
1 x 10-9
3 x 10-9
5 x 10-7 		1.32 [1.25-1.39]
1.22 [1.15-1.28]
1.28 [1.20-1.38]
1.29 [1.19-1.40]
1.2 [1.13-1.28]
1.17 [1.10-1.24]		 Illumina
[831,534] (imputed)		 N
05/03/10 The Normal Tension Glaucoma Genetic Study Group of Japan Glaucoma Society
April 02, 2010
Opthamology
Genome-wide Association Study of Normal Tension Glaucoma: Common Variants in SRBD1 and ELOVL5 Contribute to Disease Susceptibility 		Glaucoma 305 Japanese cases, 355 Japanese controls NR 2p21
6p12.1		 SRBD1
ELOVL5		 rs3213787-A
rs735860-C		 0.81
0.48		 3 x 10-9
4 x 10-6 		2.8 [1.96-3.99]
1.69 [1.36-2.11]		 Affymetrix
[325,947]		 N
05/11/10 Liu
April 01, 2010
Twin Res Hum Genet
Genome-Wide Association Study of Height and Body Mass Index in Australian Twin Families 		Body mass index 11,536 European descent family members NR 6q22.33
10p15.1		 LAMA2
Intergenic		 rs2275215-T
rs10458787-G		 0.73
0.76		 4 x 10-7
1 x 10-6 		.09 [0.05-0.13] SD decrease
.09 [0.04-0.14] SD increase		 Illumina
[559,712] (imputed)		 N
05/11/10 " Height 11,536 European descent family members NR 4q31.21
6q24.1
2p16.1
12q14.3
15q25.2
15q25.2
6p21.31
4p15.31		 HHIP
GPR126
EFEMP1
HMGA2
ADAMTSL3
SH3GL3,ADAMTSL3
HMGA1
LC0RL		 rs1812175-C
rs6570507-G
rs3791675-C
rs8756-A
rs7183263-G
rs10906982-A
rs1776897-T
rs6830062-T		 0.83
0.71
0.77
0.51
0.52
0.52
0.49
0.84		 1 x 10-9
2 x 10-7
3 x 10-7
4 x 10-7
4 x 10-7
5 x 10-7
7 x 10-6
8 x 10-6 		.12 [0.07-0.17] SD decrease
.08 [0.04-0.12] SD increase
.09 [0.04-0.14] SD increase
.07 [0.03-0.11] SD decrease
.07 [0.03-0.11] SD increase
.07 [0.03-0.11] SD increase
.11 [0.04-0.18] SD decrease
.09 [0.04-0.14] SD increase		 Illumina
[559,712] (imputed)		 N
05/03/10 Uher
April 01, 2010
Am J Psychiatry
Genome-Wide Pharmacogenetics of Antidepressant Response in the GENDEP Project 		Response to antidepressants 706 European descent individuals NR 6q25.1
1p22.2
10p12.31
19p13.11
19q13.42
1q25.3
18q12.1
6q25.1		 UST
Intergenic
Intergenic
SLC27A1
IL11
RGL1
Intergenic
UST		 rs2500535-A
rs2136093-?
rs16920624-?
rs11666579-?
rs1126757-?
rs4651156-?
rs1013696-?
rs2500535-A		 0.06
0.31
0.07
0.48
0.48
0.29
0.22
0.06		 4 x 10-8 (nortriptyline)
4 x 10-7 (whole sample)
7 x 10-7 (whole sample)
3 x 10-6 (genotype x drug)
3 x 10-6 (escitalopram)
3 x 10-6 (nortriptyline)
4 x 10-6 (genotype x drug)
9 x 10-6 (genotype x drug)		 27 [NR] % worse outcome
8.3 [NR] % worse outcome
16 [NR] % worse outcome
14.4 [NR] % better outcome
10.4 [NR] % better outcome
12.6 [NR] % worse outcome
17.8 [NR] % worse outcome
29.7 [NR] % worse outcome		 Illumina
[539,391]		 N
04/20/10 Yoshida
April 01, 2010
Int J Mol Med
Association of genetic variants with myocardial infarction in Japanese individuals with different lipid profiles 		Myocardial infarction 1,188 Japanese cases, 4,082 Japanese controls NR NS NS NS NS NS NS Affymetrix
[~500,000]		 N
04/15/10 Liu
March 30, 2010
Mol Psychiatry
Meta-analysis of genome-wide association data of bipolar disorder and major depressive disorder 		Bipolar disorder and major depressive disorder (combined) 4,387 Caucasian bipolar cases, 6,209 Caucasian controls, 1,695 Dutch MDD cases, 1,761 Dutch controls NR 12p13.33
10q21.2
15q14
6q25.2
7q21.12
2q31.1
18p11.32
13q14.3
4q28.1		 CACNA1C
ANK3
C15orf53
SYNE1
C7orf23,DMTF1
Intergenic
COLEC12,THOC1
Intergenic
FAT4		 rs1006737-A
rs10994338-A
rs12912251-T
rs17082664-G
rs11773103-G
rs4972755-A
rs7226677-G
rs1262778-C
rs1395241-G		 0.36
NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-8
5 x 10-7
1 x 10-6
1 x 10-6
1 x 10-6
3 x 10-6
4 x 10-6
8 x 10-6
8 x 10-6 		1.18 [NR] (bipolar)
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix & Perlegen
[1,472,580] (imputed)		 N
04/14/10 Kiemeney
March 28, 2010
Nat Genet
A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer 		Urinary bladder cancer 611 Icelandic cases, 37,478 Icelandic controls, 1,278 Dutch cases, 1,832 Dutch controls 771 English cases, 574 English controls, 515 Italian cases, 584 English controls, 201 Belgian cases, 385 Belgian controls, 214 Eastern European cases, 533 Eastern European controls, 352 Swedish cases, 1,350 Swedish controls, 246 Spanish cases, 890 Spanish controls, 217 German cases, 202 German controls, 334 Dutch cases, 1,721 Dutch controls 8q24.21
4p16.3
3q28		 MYC
TACC3,TMEM129,SLBP,FGFR3
TP63		 rs9642880-T
rs798766-T
rs710521-A		 0.44
0.19
0.73		 7 x 10-12
1 x 10-11
6 x 10-8 		1.21 [1.15-1.28]
1.24 [1.17-1.32]
1.19 [1.12-1.27]		 Illumina
[304,703]		 N
04/13/10 Arking
March 25, 2010
PLoS One
Genome-wide Association Study Identifies GPC5 as a Novel Genetic Locus Protective against Sudden Cardiac Arrest 		Sudden cardiac arrest 424 Caucasian cases, 226 Caucasian controls 19,611 individuals NS NS NS NS NS NS Affymetrix
[1,966,233] (imputed)		 N
04/12/10 Azzato
March 23, 2010
Cancer Epidemiol Biomarkers Prev
A Genome-Wide Association Study of Prognosis in Breast Cancer 		Breast cancer (prognosis) 1,145 women 4,335 British women NS NS NS NS NS NS Illumina
[528,252]		 N
04/14/10 Barber
March 22, 2010
PLoS ONE
Genome-wide association of lipid-lowering response to statins in combined study populations 		Response to statin therapy 3,928 Caucasian individuals NR 14q32.13
8p12
2q37.2
4q35.2
2q22.3
6p22.3
3p26.3
1q42.2
6q15
9q33.2
12p12.1
1p36.32
2p21
11q12.2
4q35.2
1p13.3
1q31.2
20q13.31
6q13
13q31.1
2q14.3
2q24.3
9q21.33
11q12.2
7p21.1
8q24.13
10p15.3
10q21.3
16q24.1
1p32.3
21q21.3
2p24.1
3p26.3
7q11.21
2q24.1
7p21.2 - p21.1		 CLMN, FLJ45244, DICER1
LOC646909, DUSP4, KIF13B
ASB18,LOC728087,IQCA
LOC644282,LOC644325,MRPS36P2
ACVR2A, ORC4L, LOC647065
LOC729105, ID4, MBOAT1
LOC402123, CNTN6, CHL1
DISC1, SIA1L2, DISC2
RNGTT, ACTBP8, LOC644119
MIRN147, CDK5RAP2, MEGF9
SOX5, FLJ32894, BCAT1
PRDM16,ARHGEF16,MEFGF6
TTC7A,MCFD2,FLJ40172
FADS2, FADS1, FADS3
LOC544042, F11, KLKB1
CELSR2,PSRC1, SORT1
FAM5C,LOC647132
HMG1L1,CTCFL,RBM38
BAI3, LMBRD1, COL19A1
LOC390415, LOC647298, C13orf7
CNTNAP5
COBLL1, LOC728184, GRB14
SLC28A3, RMI1, LOC729388
FADS2, FADS1, FEN
LOC402642, ABCB5, SP8
TRIB1, NSMCE2, KIAA0196
LOC727878,LOC728209,LOC441546
ANXA2P3, LOC645084, RPL7AP1
LOC401864, LOC283904, LOC729464
GLIS1,DMRTB1,FLJ40434
GRIK1, CLDN17, CLDN8
APOB, FLJ21820, GDF7
CNTN6,LOC402123,CHL1
ZNF679, LOC728927, LOC442320
NR4A2, GPD2, LOC728038
SOSTDC1,LOC442511,LOC729920		 rs8014194-A
rs10091038-A
rs13390159-A
rs1431005-A
rs7584099-G
rs16883019-C
rs4684585-G
rs10746514-A
rs12527253-G
rs16909449-C
rs7979575-C
rs6658356-A
rs17540621-C
rs174583-T
rs13148903-G
rs646776-C
rs2053302-T
rs6070116-G
rs3757057-T
rs1218282-C
rs2901331-A
rs10221833-C
rs10123041-T
rs1535-G
rs10950821-G
rs2954038-C
rs729397-C
rs7900909-C
rs11641231-G
rs6588480-A
rs9305406-G
rs541041-G
rs35964523-T
rs10266483-A
rs16839962-T
rs10270805-A		 0.24
0.43
0.16
0.4
0.41
0.04
0.43
0.42
0.34
0.25
0.16
0.06
0.06
0.34
0.25
0.19
0.18
0.25
0.05
0.06
0.31
0.09
0.16
0.32
0.26
0.32
0.26
0.15
0.23
0.15
0.2
0.16
0.42
0.35
0.13
0.07		 2 x 10-8 (chol, diff)
3 x 10-8 (HDL, sum)
2 x 10-7 (LDL, diff)
2 x 10-7 (LDL, diff)
5 x 10-7 (Triglyceride, diff)
7 x 10-7 (Triglyceride, sum)
9 x 10-7 (LDL, sum)
1 x 10-6 (LDL, sum)
1 x 10-6 (LDL, sum)
1 x 10-6 (Triglyceride, sum)
2 x 10-6 (Triglyceride, sum)
2 x 10-6 (chol, sum)
2 x 10-6 (chol, sum)
3 x 10-6 (Triglyceride, sum)
3 x 10-6 (LDL, sum)
4 x 10-6 (chol, sum)
4 x 10-6 (chol, sum)
4 x 10-6 (chol, sum)
4 x 10-6 (Triglyceride, sum)
5 x 10-6 (Triglyceride, sum)
6 x 10-6 (Triglyceride, sum)
6 x 10-6 (Triglyceride, sum)
6 x 10-6 (HDL, sum)
7 x 10-6 (HDL, sum)
7 x 10-6 (chol, sum)
7 x 10-6 (Triglyceride, sum)
8 x 10-6 (chol, sum)
8 x 10-6 (LDL, sum)
8 x 10-6 (HDL, sum)
8 x 10-6 (chol, sum)
8 x 10-6 (Triglyceride, sum)
8 x 10-6 (LDL, sum)
8 x 10-6 (chol, sum)
8 x 10-6 (LDL, sum)
9 x 10-6 (HDL, sum)
9 x 10-6 (chol, sum)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[~2.5 million](imputed)		 N
04/12/10 Davis
March 21, 2010
Behav Genet
A Three-Stage Genome-Wide Association Study of General Cognitive Ability: Hunting the Small Effects 		Cognitive ability 860 UK children, at least 1 SD above/below the mean 2,619 UK children NS NS NS NS NS NS Affymetrix
[358,948] (pooled)		 N
03/29/10 Li
March 19, 2010
Lancet Oncol
Genetic variants and risk of lung cancer in never smokers: a genome-wide association study. 		Lung cancer 377 cases, 377 matched controls 511 cases, 1,007 controls 13q31.3 GPC5 rs2352028-A 0.26 6 x 10-6 1.46 [1.26-1.70] Illumina
[331,918]		 N
04/12/10 Houlihan
March 18, 2010
Am J Hum Genet
Common Variants of Large Effect in F12, KNG1, and HRG Are Associated with Activated Partial Thromboplastin Time 		Activated partial thromboplastin time 1,431 Scottish adults NR 5q35.3
3q27.3
3q27.3		 F12
KNG1
HRG		 rs2731672-A
rs710446-G
rs9898-T		 0.27
0.40
0.32		 2 x 10-30
1 x 10-21
1 x 10-11 		.45 [0.37-0.53] unit decrease
.36 [0.29-0.43] unit decrease
.26 [0.19-0.33] unit increase		 Illumina
[542,050]		 N
04/02/10 Medland
March 18, 2010
Am J Hum Genet
A Variant in LIN28B Is Associated with 2D:4D Finger-Length Ratio, a Putative Retrospective Biomarker of Prenatal Testosterone Exposure 		Digit length ratio 2,889 European children and adolescents 3,659 European children 6q16.3 LIN28B rs314277-A 0.15 2 x 10-6 .63 [0.41-0.85] increase in mean 2D:4D Illumina
[310,613]		 N
04/02/10 Nakajima
March 18, 2010
PLoS ONE
New Sequence Variants in HLA Class II/III Region Associated with Susceptibility to Knee Osteoarthritis Identified by Genome-Wide Association Study 		Knee osteoarthritis 899 Japanese cases, 3,396 Japanese controls 167 Japanese cases, 347 Japanese controls, 243 Spanish cases, 426 Spanish controls, 570 Greek cases, 645 Greek controls 6p21.32 BTNL2, HLA-DQA2, HLA-DQB1 rs10947262-T 0.42 5 x 10-9 1.31 [1.20-1.44] Illumina
[459,393]		 N
04/12/10 Newman
March 18, 2010
J Gerontol A Biol Sci Med Sci
A Meta-analysis of Four Genome-Wide Association Studies of Survival to Age 90 Years or Older: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium 		Longevity 1,836 long-lived Caucasian individuals, 1,955 Caucasian controls 2,594 long-lived Caucasian individuals, 3,431 Caucasian controls 10q23.2 MINPP1 rs9664222-C 0.79 7 x 10-7 1.22 [NR] Affymetrix and Illumina
[2,287,520] (imputed)		 N
04/08/10 Bozaoglu
March 17, 2010
J Clin Endocrinol Metab
Chemerin, a Novel Adipokine in the Regulation of Angiogenesis 		Plasma chemerin levels 1,354 Mexican-American family members NR 5q14.3
9q22.32
6p21.2
1q23.2
1q23.2
12q21.1
7q31.33		 EDIL3
PTCH
PI16
OR10J3
OR10J1
TRHDE
GRM8		 rs347344-?
rs10988802-?
rs1405069-?
rs6687840-?
rs4446959-?
rs7963521-?
rs11971186-?		 NR
NR
NR
NR
NR
NR
NR		 1 x 10-6
4 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR		 Illumina
[542,944]		 N
03/26/10 Smith
March 15, 2010
Circulation
Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium. 		Plasma coagulation factors Up to 23,608 European ancestry individuals Up to 7,604 European ancestry individuals 20q11.22
6q24.3		 PROCR
STXBP5		 rs867186-G
rs9390459-A		 0.101
0.442		 6 x 10-37 (FVII)
1 x 10-22 (vWF)		 NR
4.8 [2.1-7.5] % decrease		 Affymetrix & Illumina
[~2.6 million] (imputed)		 N
03/24/10 Franke
March 14, 2010
Nat Genet
Genome-wide association study for ulcerative colitis identifies risk loci at 7q22 and 22q13 (IL17REL). 		Ulcerative colitis 1,043 German cases, 1,703 German controls 2,539 European descent cases, 5,428 European descent controls 1p36.13
6p21.32
1q32.1
7q22.1
22q13.33
10q24.2		 OTUD3
HLA-DRA
IL10
SMURF1,KPNA7
IL17REL
NKX2-3		 rs4654925-G
rs9268923-C
rs3024493-T
rs7809799-G
rs5771069-G
rs6584283-T		 0.52
0.67
0.16
0.04
0.49
0.46		 9 x 10-22
4 x 10-15
1 x 10-12
9 x 10-11
4 x 10-8
2 x 10-6 		1.41 [1.30-1.54]
1.45 [1.33-1.59]
1.35 [1.22-1.50]
1.56 [1.36-1.78]
1.17 [1.11-1.25]
1.22 [1.12-1.32]		 Affymetrix
[1,897,764] (imputed)		 N
04/02/10 McGovern
March 14, 2010
Nat Genet
Genome-wide association identifies multiple ulcerative colitis susceptibility loci 		Ulcerative colitis 2,693 European descent cases, 6,791 European descent controls 2,009 European descent cases, 1,580 European descent controls 1p36.13
1p31.3
12q15
1p36.13
5p15.33
1q23.3
3p21.31
2p16.1
10q24.2
1q32.1
17q12
9q34.3
7q31.1
17q12
1q32.1
21q21.1
9p24.1
16p13.13
2q33.1		 RNF186,OTUD3,PLA2G2E
IL23R
IFNG,IL26
RNF186,OTUD3,PLA2G2E
CEP72,TPPP
FCGR2A,FCGR2C
MST1
REL,CCDC139,PUS10
NKX2-3
IL10,IL19
ORMDL3,ZPBP2M,GSDML
CARD9
DLD,LAMB1
GSDMB
K1F21B
NR
JAK2
CIITA
SATB2		 rs6426833-A
rs2201841-A
rs1558744-A
rs1317209-T
rs4957048-C
rs10800309-A
rs3197999-T
rs13003464-G
rs11190140-T
rs3024505-T
rs2305480-A
rs4077515-C
rs4598195-A
rs8067378-A
rs11584383-T
rs1736135-T
rs10758669-C
rs4781011-T
rs1992950-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-21
1 x 10-13
4 x 10-12
2 x 10-10
1 x 10-9
3 x 10-9
4 x 10-9
7 x 10-9
1 x 10-8
1 x 10-8
3 x 10-8
5 x 10-8
8 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
1 x 10-6
3 x 10-6
5 x 10-6 		1.3 [NR]
1.27 [NR]
1.16 [NR]
1.17 [NR]
1.3 [NR]
1.2 [NR]
1.2 [NR]
1.13 [NR]
1.2 [NR]
1.23 [NR]
1.15 [NR]
1.14 [NR]
1.09 [NR]
1.12 [NR]
1.27 [NR]
1.2 [NR]
1.22 [NR]
1.12 [NR]
1.1 [NR]		 Affymetrix
[266,047]		 N
03/30/10 Pattaro
March 11, 2010
BMC Med Genet
A meta-analysis of genome-wide data from five European isolates reveals an association of COL22A1, SYT1, and GABRR2 with serum creatinine level 		Serum creatinine 4,006 European individuals 2,035 European individuals NS NS NS NS NS NS Illumina
[~322,498]		 N
03/30/10 Buil
March 08, 2010
Blood
C4BPB/C4BPA is a new susceptibility locus for venous thrombosis with unknown protein S independent mechanism: results from genome-wide association and gene expression analyses followed by case-control studies. 		Plasma C4b binding protein levels 352 related Spanish individuals NR 1q32.2 C4BPB, C4BPA rs3813948-C 4 x 10-10 (%a7b0) NR Illumina
[283,437]		 N
03/30/10 Rothenberg
March 07, 2010
Nat Genet
Common variants at 5q22 associate with pediatric eosinophilic esophagitis. 		Eosinophilic esophagitis (pediatric) 181 European descent adolescent cases, 1,974 European descent adolescent controls 170 European descent cases, 1,130 European descent controls 5q22.1
16q24.1
3q26.32
4q21.1
12q13.3
5q14.2
11q21
4q21.1
6p11.2
17q24.3
8q22.2
18q12.1
8q24.12
10q23.1		 WDR36
NR
NR
NR
STAT6
NR
NR
NR
NR
NR
NR
DSG1
NR
NR		 rs3806932-?
rs371915-?
rs6799767-?
rs1986734-?
rs167769-T
rs1032757-T
rs1939875-T
rs13106227-?
rs9500256-?
rs6501384-T
rs13278732-T
rs7236477-G
rs11989782-A
rs2224865-G		 0.54
0.87
0.58
0.49
0.37
0.07
0.26
0.62
0.58
0.33
0.27
0.03
0.23
0.31		 3 x 10-9
2 x 10-8
4 x 10-7
1 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
9 x 10-6 		1.85
1.9 [1.44-2.50]
1.49 [1.18-1.85]
1.54 [1.22-1.89]
1.36 [1.10-1.69]
1.96 [1.40-2.74]
1.54 [1.22-1.93]
1.52 [1.20-1.92]
2.04 [1.52-2.70]
1.41 [1.13-1.76]
1.31 [1.04-1.65]
2.22 [1.39-3.55]
1.53 [1.21-1.93]
1.44 [1.15-1.79]		 Illumina
[~550,000]		 N
04/06/10 Adkins
March 02, 2010
Mol Psychiatry
Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs 		Response to antipsychotic treatment 738 European American, African American, and other schizophrenia cases NR 15q14
5q14.3
4q24
7q22.3
12p12.1
18q12.2
2p25.3
13q12.11
14q32.13
2p25.1
10p11.22
11q23.1
2p24.1
8q22.3
9q33.1
16q23.3
7p21.1
9q31.1
2p12
5q31.3
6p21.31
2p12
16p13.13
2p16.1
1p31.1
10p12.33
16q23.3
18q22.2
4q23
16p13.12
18q22.2
1p21.2
11q24.2
20q13.2
2p11.2
2q33.1
6q14.3		 MEIS2
GPR98
Intergenic
PRKAR2B
SOX5
FHOD3
Intergenic
Intergenic
CLMN
RNF144A
Intergenic
Intergenic
Intergenic
Intergenic
ASTN2
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
PPARD
Intergenic
ATF7IP2
Intergenic
Intergenic
Intergenic
CDH13
Intergenic
Intergenic
LOC729993
Intergenic
Intergenic
KIRREL3
Intergenic
Intergenic
Intergenic
Intergenic		 rs1568679-?
rs1967256-?
rs1405687-?
rs13224682-?
rs1464500-?
rs17651157-?
rs6735179-?
rs518590-?
rs1187614-?
rs6741819-?
rs2994684-?
rs7105881-?
rs1117324-?
rs977396-?
rs4838255-?
rs4783227-?
rs10499504-?
rs320209-?
rs399885-?
rs17100498-?
rs9658108-?
rs7570469-?
rs13335336-?
rs10202231-?
rs11163585-?
rs17661538-?
rs17216786-?
rs8092443-?
rs11735070-?
rs153091-?
rs11663206-?
rs17410015-?
rs620875-?
rs6092078-?
rs1534238-?
rs17385675-?
rs1577917-?		 0.103
0.148
0.088
0.072
0.232
0.068
0.346
0.21
0.313
0.305
0.155
0.367
0.156
0.089
0.139
0.424
0.11
0.068
0.327
0.126
0.052
0.418
0.078
0.457
0.24
0.138
0.054
0.225
0.338
0.227
0.289
0.063
0.101
0.115
0.381
0.069
0.21		 1 x 10-8 (risperidone-hip circumference)
3 x 10-8 (olanzapine-hemoglobin A1c
5 x 10-8 (ziprasidone-hip circumference)
6 x 10-8 (clozapine-triglycerides)
1 x 10-7 (perphenazine-HDL)
1 x 10-7 (perphenazine-triglycerides)
1 x 10-7 (perphenazine-triglycerides)
2 x 10-7 (quetiapine-HDL)
2 x 10-7 (perphenazine-total cholesterol)
2 x 10-7 (perphenazine-triglycerides)
3 x 10-7 (clozapine-triglycerides)
3 x 10-7 (risperidone-hip circumference)
3 x 10-7 (risperidone-hip circumference)
3 x 10-7 (olanzapine-total cholesterol)
3 x 10-7 (perphenazine-triglycerides)
4 x 10-7 (olanzapine-total cholesterol)
4 x 10-7 (clozapine-total cholesterol)
4 x 10-7 (clozapine-glucose)
5 x 10-7 (clozapine-heart rate)
5 x 10-7 (risperidone-hemoglobin A1c)
5 x 10-7 (clozapine-glucose)
6 x 10-7 (clozapine-heart rate)
7 x 10-7 (risperidone-hemoglobin A1c)
7 x 10-7 (perphenazine-triglycerides)
9 x 10-7 (perphenazine-HDL)
1 x 10-6 (clozapine-triglycerides)
1 x 10-6 (clozapine-triglycerides)
1 x 10-6 (risperidone-hemoglobin A1c)
1 x 10-6 (perphenazine-triglycerides)
2 x 10-6 (perphenazine-triglycerides)
2 x 10-6 (risperidone-hemoglobin A1c)
2 x 10-6 (perphenazine-triglycerides)
3 x 10-6 (clozapine-triglycerides)
3 x 10-6 (risperidone-hip circumference)
3 x 10-6 (clozapine-triglycerides)
3 x 10-6 (clozapine-triglycerides)
3 x 10-6 (clozapine-triglycerides)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[492,900]		 N
03/25/10 Bierut
March 02, 2010
Proc Natl Acad Sci U S A
A genome-wide association study of alcohol dependence 		Alcohol dependence 1,235 European American cases, 662 African American cases, 1,433 European American controls, 499 African American controls 219 European American families, 35 African American families, 4 other families, 487 German cases, 1,358 German controls NS NS NS NS NS NS Illumina
[948,658]		 N
03/29/10 Edenberg
March 01, 2010
Alcohol Clin Exp Res
Genome-Wide Association Study of Alcohol Dependence Implicates a Region on Chromosome 11 		Alcohol dependence 847 European descent cases, 552 European descent controls, 345 African American cases, 140 African American controls 262 families NS NS NS NS NS NS Illumina
[up to 941,298]		 N
07/04/10 Joubert
March 01, 2010
Genome Med
A whole genome association study of mother-to-child transmission of HIV in Malawi 		HIV (mother-to-child transmission) 100 Malawian infant cases, 126 Malawian infant controls NR NS NS NS NS NS NS Illumina
[586,681]		 N
03/29/10 Uhl
March 01, 2010
Pharmacogenomics
Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement 		Smoking cessation 108 quitters, 216 nonquitters NR NS NS NS NS NS NS Affymetrix 6.0
[NR] (pooled)		 N
03/29/10 Dubois
February 28, 2010
Nat Genet
Multiple common variants for celiac disease influencing immune gene expression. 		Celiac disease 4,533 European descent cases, 10,750 European descent controls 4,918 European descent cases, 5,684 European descent controls 6p21.32
3q28
3q25.33
4q27
12q24.12
6q23.3
1q31.2
3p21.31
11q24.3
2q12.1
6q25.3
6q22.33
2p16.1
2q31.3
1p36.11
18p11.21
6q15
10q22.3
21q22.3
1p36.32
3p22.3
8q24.21
1q32.1
2q33.2
2p14
3q13.33
16p13.13
6p25.3
Xp22.2
1p36.23
1p31.3
22q11.21
3p14.1
7p14.1
14q24.1
1q24.2
3q26.2
13q14.2
17q21.31
1q24.3		 HLA-DQA1, HLA-DQB1
LPP
IL12A
IL2, IL21
SH2B3
TNFAIP3
RGS1
CCR1, CCR2, CCRL2, CCR3, CCR5, CCR9
ETS1
IL18RAP, IL18R1, IL1RL1, IL1RL2
TAGAP
PTPRK, THEMIS
REL, AHSA2
ITGA4, UBE2E3
RUNX3
PTPN2
BACH2, MAP3K7
ZMIZ1
ICOSLG
TNFRSF14, MMEL1
CCR4
Intergenic
Intergenic
CTLA4, ICOS, CD28
PLEK
CD80, KTELC1
CIITA, SOCS1, CLEC16A
IRF4
TLR7, TLR8
PARK7, TNFRSF9
NFIA
UBE2L3, YDJC
FRMD4B
ELMO1
ZFP36L1
CD247
Intergenic
Intergenic
Intergenic
FASLG, TNFSF18, TNFSF4		 rs2187668-A
rs1464510-A
rs17810546-G
rs13151961-?
rs653178-G
rs2327832-G
rs2816316-?
rs13098911-A
rs11221332-A
rs917997-A
rs1738074-A
rs802734-G
rs13003464-G
rs13010713-G
rs10903122-?
rs1893217-G
rs10806425-A
rs1250552-?
rs4819388-?
rs3748816-?
rs13314993-C
rs9792269-?
rs296547-?
rs4675374-A
rs17035378-?
rs11712165-C
rs12928822-?
rs1033180-A
rs5979785-?
rs12727642-A
rs6691768-?
rs2298428-A
rs6806528-A
rs6974491-A
rs4899260-A
rs864537-?
rs10936599-A
rs2762051-A
rs2074404-?
rs859637-A		 0.26
0.49
0.13
0.86
0.50
0.22
0.84
0.10
0.24
0.24
0.43
0.31
0.40
0.45
0.52
0.17
0.40
0.53
0.72
0.66
0.46
0.76
0.64
0.22
0.72
0.39
0.84
0.08
0.74
0.19
0.62
0.20
0.10
0.17
0.26
0.61
0.25
0.18
0.75
0.49		 1 x 10-50
3 x 10-40
4 x 10-28
2 x 10-27
7 x 10-21
4 x 10-19
2 x 10-17
3 x 10-17
5 x 10-16
1 x 10-15
3 x 10-15
3 x 10-14
4 x 10-13
5 x 10-11
2 x 10-10
3 x 10-10
4 x 10-10
9 x 10-10
2 x 10-9
3 x 10-9
3 x 10-9
3 x 10-9
4 x 10-9
6 x 10-9
8 x 10-9
8 x 10-9
3 x 10-8
6 x 10-8
6 x 10-8
9 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
2 x 10-7
4 x 10-7
4 x 10-7
5 x 10-7
7 x 10-7
1 x 10-6
2 x 10-6 		6.23 [5.95-6.52]
1.29 [1.25-1.34]
1.36 [1.29-1.44]
1.35 [1.28-1.43]
1.2 [1.15-1.24]
1.23 [1.17-1.28]
1.25 [1.19-1.32]
1.3 [1.23-1.39]
1.21 [1.16-1.27]
1.19 [1.14-1.25]
1.16 [1.12-1.21]
1.17 [1.12-1.22]
1.15 [1.11-1.20]
1.13 [1.09-1.18]
1.12 [1.09-1.18]
1.17 [1.12-1.23]
1.13 [1.09-1.17]
1.12 [1.09-1.16]
1.14 [1.09-1.19]
1.12 [1.09-1.18]
1.13 [1.08-1.17]
1.14 [1.10-1.19]
1.12 [1.09-1.16]
1.14 [1.09-1.19]
1.14 [1.09-1.19]
1.13 [1.08-1.17]
1.16 [1.10-1.22]
1.21 [1.13-1.29]
1.14 [1.09-1.19]
1.14 [1.09-1.20]
1.11 [1.06-1.15]
1.13 [1.08-1.19]
1.19 [1.12-1.27]
1.14 [1.09-1.20]
1.12 [1.07-1.16]
1.1 [1.06-1.15]
1.12 [1.07-1.16]
1.13 [1.08-1.18]
1.11 [1.06-1.16]
1.1 [1.06-1.14]		 Illumina
[292,387]		 N
03/25/10 Okada
February 26, 2010
Hum Mol Genet
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. 		Height 19,633 Japanese individuals NR 4p15.32
6p21.31
8q12.1
2p16.1
3q23
2q37.1
9q34.3
12q23.2
15q24.2
2p22.3
15q25.2
1p36.13
15q21.2
7p22.3
12q13.13
10q26.13
20q11.22
13q31.3
18q11.2
2q35
7p15.3
16q23.3
13q14.11
16p13.11
1q25.3		 NCAPG, LCORL
HMGA1
PLAG1
EFEMP1
ZBTB38
DIS3L2
LHX3, QSOX2
IGF1
SIN3A, PTPN9
LTBP1
ADAMTSL3
ATP13A2, SDHB
CYP19A1
GNA12
ATF7, ATP5G2
PLEKHA1
GDF5, UQCC
GPC5
CABLES1
IHH
CDCA7L
CDH13
DGKH
PDXDC1, NTAN1
GLT25D2		 rs7678436-A
rs7742369-G
rs7833986-A
rs3791679-A
rs9825379-A
rs7571816-A
rs12338076-C
rs5742692-G
rs4886707-T
rs3769528-G
rs4842838-G
rs3738814-A
rs2305707-G
rs798497-G
rs11170631-C
rs6585827-G
rs2236164-C
rs8002779-A
rs4369779-T
rs16859517-T
rs1175000-C
rs6563943-A
rs6561030-A
rs1136001-T
rs756199-G		 0.26
0.14
0.08
0.25
0.24
0.45
0.34
0.27
0.42
0.15
0.29
0.35
0.37
0.27
0.36
0.43
0.22
0.48
0.20
0.39
0.40
0.32
0.28
0.44
0.42		 8 x 10-15
1 x 10-13
8 x 10-10
6 x 10-9
6 x 10-9
9 x 10-9
2 x 10-8
4 x 10-8
8 x 10-8
8 x 10-8
1 x 10-7
2 x 10-7
7 x 10-7
7 x 10-7
9 x 10-7
2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
7 x 10-6 		.09 [0.07-0.11] cm decrease
.11 [0.08-0.14] cm increase
.12 [0.08-0.16] cm decrease
.07 [0.05-0.09] cm increase
.07 [0.05-0.09] cm increase
.06 [0.04-0.08] cm increase
.06 [0.04-0.08] cm increase
.07 [0.05-0.09] cm decrease
.06 [0.04-0.08] cm increase
.08 [0.05-0.11] cm decrease
.06 [0.04-0.08] cm decrease
.06 [0.04-0.08] cm increase
.06 [0.04-0.07] cm decrease
.06 [0.04-0.08] cm decrease
.05 [0.03-0.07] cm increase
.05 [0.03-0.07] cm decrease
.06 [0.04-0.08] cm increase
.05 [0.03-0.07] cm decrease
.06 [0.04-0.08] cm decrease
.05 [0.03-0.07] cm increase
.05 [0.03-0.07] cm increase
.05 [0.03-0.07] cm increase
.05 [0.03-0.07] cm decrease
.05 [0.03-0.07] cm decrease
.05 [0.03-0.07] cm increase		 Illumina
[420,885]		 N
03/25/10 Pillas
February 26, 2010
PLoS Genet
Genome-wide association study reveals multiple loci associated with primary tooth development during infancy. 		Primary tooth development (number of teeth) 5,752 European descent related individuals NR 17q24.3
Xq13.1
17q21.32
14q24.1
2q35
17q21.32
12q14.3
6q22.31
12q14.3		 KCNJ2
EDA
IGF2BP1
RAD51L1
Intergenic
HOXB1, HOXB2
MSRB3
Intergenic
HMGA2		 rs8079702-G
rs4844096-G
rs9674544-G
rs1956529-T
rs6435957-T
rs6504340-G
rs10506525-C
rs2817937-C
rs12424086-C		 0.39
0.42
0.46
0.38
0.37
0.22
0.27
0.12
0.23		 1 x 10-14
5 x 10-11
2 x 10-8
3 x 10-8
4 x 10-7
6 x 10-7
9 x 10-7
3 x 10-6
4 x 10-6 		1.15 [NR] % variance explained
.73 [NR] % variance explained
.27 [NR] % variance explained
.51 [NR] % variance explained
.37 [NR] % variance explained
.44 [NR] % variance explained
.18 [NR] % variance explained
.25 [NR] % variance explained
.22 [NR] % variance explained		 Illumina
[300,766]		 N
03/25/10 " Primary tooth development (time to first tooth eruption) 5,919 European descent related individuals NR 17q24.3
Xq13.1
12q14.3
6q21
17q21.32
12q14.3		 KCNJ2
EDA
MSRB3
Intergenic
IGF2BP1
HMGA2		 rs8079702-G
rs5936487-G
rs10506525-C
rs9386463-G
rs9674544-G
rs12424086-C		 0.39
0.39
0.27
0.45
0.46
0.23		 4 x 10-22
6 x 10-11
6 x 10-9
6 x 10-7
8 x 10-7
8 x 10-6 		1.62 [NR] % variance explained
.5 [NR] % variance explained
.46 [NR] % variance explained
.38 [NR] % variance explained
.25 [NR] % variance explained
.29 [NR] % variance explained		 Illumina
[300,766]		 N
03/25/10 Han
February 25, 2010
Leuk Res
Genome-wide association study of childhood acute lymphoblastic leukemia in Korea 		Acute lymphoblastic leukemia (childhood) 45 Korean cases, 48 Korean controls NR NS NS NS NS NS NS Affymetrix
[681,931]		 N
03/25/10 Athanasiu
February 23, 2010
J Psychiatr Res
Gene variants associated with schizophrenia in a Norwegian genome-wide study are replicated in a large European cohort. 		Schizophrenia 201 Caucasian cases, 305 European controls 2,663 European cases, 13,780 European controls 9p21.2
16p12.3
10q21.2		 PLAA
ACSM1
ANK3		 rs7045881-?
rs433598-T
rs10761482-?		 NR
NR
NR		 2 x 10-6
3 x 10-6
8 x 10-6 		1.16 [NR]
1.13 [NR]
1.16 [NR]		 Affymetrix
[572,888]		 N
03/17/10 Qi
February 22, 2010
Hum Mol Genet
Genetic variants in ABO blood group region, plasma soluble E-selectin levels and risk of type 2 diabetes. 		Plasma E-selectin levels 1,005 European ancestry women 518 European ancestry women 9q34.2 ABO rs651007-T 0.22 2 x 10-82 9.71 [NR] % variance explained Affymetrix
[721,316]		 N
03/17/10 Sun
February 22, 2010
Hum Mol Genet
Genome-wide association study identifies polymorphisms in LEPR as determinants of plasma soluble leptin receptor levels. 		Soluble leptin receptor levels 1,504 European ancestry women 875 Cypriot adolescent males 1p31.3 LEPR rs1751492-C 0.30 6 x 10-13 (Nurses Health Study) 7.6 [5.64-9.56] % decrease Affymetrix
[2,543,887] (imputed)		 N
03/17/10 Cho
February 21, 2010
Nat Genet
Variants in FAM13A are associated with chronic obstructive pulmonary disease. 		Chronic obstructive pulmonary disease 2,940 white cases, 1,380 white controls 502 non-Hispanic Caucasian cases, 504 non-Hispanic Caucasian controls, 1,100 probands, 2,698 relatives 4q22.1
15q25.1
4q31.21		 FAM13A
CHRNA3, CHRNA5, IREB2
HHIP		 rs7671167-?
rs13180-?
rs13118928-?		 0.48
0.36
0.40		 1 x 10-11
2 x 10-8
5 x 10-7 		1.32 [1.19-1.47]
1.3 [1.18-1.43]
1.25 [1.14-1.37]		 Illumina
[499,578]		 N
03/15/10 Ellinor
February 21, 2010
Nat Genet
Common variants in KCNN3 are associated with lone atrial fibrillation. 		Atrial fibrillation 1,335 European descent cases, 12,844 European descent controls 1,164 European descent cases, 3,607 European descent controls 4q25
1q21.3
20q13.13		 PITX2
KCNN3
NR		 rs6843082-G
rs13376333-T
rs13038095-?		 0.26
0.30
NR		 3 x 10-28
2 x 10-21
2 x 10-7 		2.03 [1.79-2.30]
1.52 [1.40-1.64]
1.47 [1.39-1.54]		 Affymetrix and Illumina
[~2.5 million] (imputed)		 N
03/17/10 Tsai
February 19, 2010
PLoS Genet
A genome-wide association study identifies susceptibility variants for type 2 diabetes in Han Chinese. 		Type 2 diabetes 995 Han Chinese cases, 894 Han Chinese controls 1,803 Han Chinese cases, 1,473 Han Chinese controls 9p24.1
11p15.4
17p13.3		 PTPRD
KCNQ1
SRR		 rs17584499-T
rs2237895-C
rs391300-G		 0.06
0.33
0.62		 9 x 10-10
1 x 10-9
3 x 10-9 		1.57 [1.36-1.82]
1.29 [1.19-1.40]
1.28 [1.18-1.39]		 Illumina
[516,737]		 N
03/15/10 Barbalic
February 18, 2010
Hum Mol Genet
Large-scale genomic studies reveal central role of ABO in sP-selectin and sICAM-1 levels. 		Soluble levels of adhesion molecules Up to 9,813 European descent individuals NR 1q24.2
9q34.2
19p13.2
1q24.2
9q34.2		 SELP
ABO
ICAM-1
SELP
ABO		 rs6136-T
rs579459-T
rs3093030-T
rs2235302-T
rs649129-T		 NR
NR
NR
NR
NR		 4 x 10-61 (P-Selectin)
2 x 10-41 (P-Selectin)
4 x 10-23 (ICAM)
4 x 10-16 (P-Selectin)
1 x 10-15 (ICAM)		 22.6 [19.86-25.34] % increase
14 [12.04-15.96] % increase
4.15 [3.33-4.97] % increase
7.3 [5.54-9.06] % decrease
3.95 [2.99-4.91] % decrease		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
03/12/10 Okada
February 18, 2010
Hum Mol Genet
Common variations in PSMD3-CSF3 and PLCB4 are associated with neutrophil count. 		Neutrophil count 5,771 Japanese individuals 1,894 Japanese individuals 20p12.2
17q21.1		 PLCB4
PSMD3, CSF3		 rs2072910-C
rs4794822-C		 0.30
0.48		 3 x 10-10
6 x 10-10 		.11 [0.07-0.15] unit decrease in log(neutrophil ct)
.1 [0.07-0.13] unit decrease in log(neutrophil ct)		 Illumina
[486,091]		 N
03/09/10 Koller
February 17, 2010
J Clin Endocrinol Metab
Genome-Wide Association Study of Bone Mineral Density in Premenopausal European-American Women and Replication in African-American Women 		Bone mineral density 1,524 European descent sisters 669 related African American women NS NS NS NS NS NS Illumina
[547,971]		 N
03/23/10 Stein
February 17, 2010
Neuroimage
Voxelwise genome-wide association study (vGWAS). 		Brain structure 740 Caucasian individuals NR 1p36.13
3p21.31
14q22.1
6q15
16p12.1
2q37.3
6q12
7q31.32
9p13.2
3p12.1
6p12.3
20q13.12
5p12
11q23.3
13q32.2
1p35.1
20p12.1
6q16.2
8q23.1		 KIAA0090, MRT04, AKR7L
Intergenic
FRMD6
Intergenic
RBBP6
BOK, THAP4
Intergenic
CADPS2
SHB
Intergenic
GLYATL3
WFDC2, SPINT3
Intergenic
Intergenic
FARP1
CSMD2
Intergenic
Intergenic
Intergenic		 rs710865-?
rs9990343-?
rs7140150-?
rs713155-?
rs11643520-?
rs12479254-?
rs11970254-?
rs2429582-?
rs7873102-?
rs10511089-?
rs9473582-?
rs11696501-?
rs4296809-?
rs490592-?
rs688872-?
rs476463-?
rs2073233-?
rs2132683-?
rs4534106-?		 0.38
0.48
0.46
0.40
0.12
0.40
0.35
0.34
0.38
0.11
0.40
0.19
0.15
0.21
0.38
0.12
0.43
0.33
0.30		 1 x 10-7
4 x 10-7
5 x 10-7
5 x 10-7
6 x 10-7
6 x 10-7
6 x 10-7
6 x 10-7
6 x 10-7
7 x 10-7
8 x 10-7
9 x 10-7
9 x 10-7
1 x 10-6
1 x 10-6
1 x 10-6
1 x 10-6
1 x 10-6
1 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[448,293]		 N
03/09/10 Van Deerlin
February 14, 2010
Nat Genet
Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions 		Frontotemporal lobar degeneration 515 European descent cases, 2,509 European descent controls 89 European descent cases, 553 European descent controls NS NS NS NS NS NS Illumina
[~500,000]		 N
03/09/10 Lange
February 13, 2010
Hum Mol Genet
Genome-wide association study of homocysteine levels in Filipinos provides evidence for CPS1 in women and a stronger MTHFR effect in young adults. 		Homocysteine levels 1,786 unrelated Filipino women 1,679 Filipino offspring 2q34 CPS1 rs7422339-A 0.24 5 x 10-9 .05 [0.03-0.07] increase in log(Hcy) Affymetrix
[2,073,674] (imputed)		 N
03/07/10 Jakkula
February 12, 2010
Am J Hum Genet
Genome-wide association study in a high-risk isolate for multiple sclerosis reveals associated variants in STAT3 gene. 		Multiple sclerosis 68 Finnish cases, 136 Finnish controls 4,570 European cases, 10,143 Finnish controls 6p21.32
17q21.2		 HLA
STAT3		 rs3135338-A
rs744166-G		 0.13
0.41		 2 x 10-25
3 x 10-10 		3.43 [NR]
1.15 [1.10-1.20]		 Illumina
[297,343]		 N
03/06/10 Yang
February 12, 2010
PLoS Genet
Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus. 		Systemic lupus erythematosus 314 Chinese cases, 1,500 Chinese controls 2,630 Chinese cases, 2,155 Chinese controls, 314 Thai cases, 519 Thai controls 10q11.23
11q24.3		 WDFY4
ETS1		 rs7097397-G
rs1128334-A		 0.28
0.35		 8 x 10-12
2 x 10-11 		1.3 [1.21-1.40]
1.29 [1.20-1.39]		 Illumina
[514,221]		 N
03/06/10 He
February 11, 2010
Arterioscler Thromb Vasc Biol
Genome-wide association study identifies variants at the IL18-BCO2 locus associated with interleukin-18 levels. 		Interleukin-18 levels 1,523 European ancestry women 435 European ancestry women 11q23.1
11q23.1		 BCO2
BCO2		 rs2115763-T
rs1834481-G		 0.33
0.24		 4 x 10-9
1 x 10-8 		NR
NR		 Affymetrix
[704,409]		 N
03/06/10 Codd
February 07, 2010
Nat Genet
Common variants near TERC are associated with mean telomere length. 		Telomere length 2,917 European individuals 9,492 European individuals 3q26.2 TERC rs12696304-G 0.30 4 x 10-14 .11 [0.08-0.14] unit decrease Affymetrix
[405,649]		 N
04/15/10 Kamatani
February 07, 2010
Nat Genet
Genome-wide association study of hematological and biochemical traits in a Japanese population 		Hematological and biochemical traits Up to ~14,700 Japanese individuals NR 6q23.3
9q34.2
6q23.3
11q23.3
12p13.31
4q12
4q12
10p12.33
16q24.3
17p13.2
9q34.2
10q11.21
3q27.3
9q34.2
6p21.1
18q12.3
3p14.1
17p11.2
3p24.2
5p15.33
10q11.23
9q34.2
12q24.12
1q31.2
6q23.3
15q22.31
1q22
2p23.3
12q24.12
12q24.12
12p13.32
10q11.23
6p21.33
6q21
20q13.31
22q11.21
6q21
15q21.3
1q44
7q21.2
12q15
15q26.2
19q13.33
3p24.2
5p15.33
8p21.3
22q13.33
2p21
2q31.1
9q34.2		 HBS1L,MYB
ABO
HBS1L,MYB
APO-A cluster
CD163
PDGFRA,HK1
PDGFRA,HK1
FAM23A,MRC1L1,FAM23B,MRC1
CDT1
GP1BA
ABO
ALOX5,MARCH8,ANUBL1,FAM21C,AGAP4
Intergenic
ABO
USP49,MED20,BYSL,CCND3
SLC14A2
Intergenic
TNFRSF13B
THRB
SLC12A7
MSMB,NC0A4, TIMM23
ABO
ALDH2
ATP6V1G3,PTPRC
HBS1L,MYB
IGDCC4,DPP8,PTPLAD1,C15orf44,SLC24A1,DENND4A
BGLAP,PAQR6,SMG5,TMEM79,C1orf85,VHLL,CCT3,C1orf182
GCKR
BRAP,ALDH2
GGT
CCND2
MSMB,NC0A4,TIMM23
CDSN,PSORS1C1
C6orf182,CD164
RBM38
HIC2, UBE2L3
C6orf182,CD164
WDR72
TRIM58
CDK6
RAP1B,NUP107,SLC35E3
Intergenic
RPL13A,RPS11,FCGRT,RCN3
THRB
TERT
DOK2,XPO7
NCAPH2,SCO2,TYMP,KLHDC7B
PRKCE
LRP2
ABO		 rs7775698-T
rs495828-T
rs7775698-T
rs7350481-G
rs7136716-G
rs218237-T
rs218237-T
rs2477664-T
rs837763-C
rs6065-T
rs495828-T
rs2279434-T
rs9820070-C
rs495828-T
rs3218097-T
rs4890568-G
rs11709625-A
rs4273077-G
rs9310736-A
rs4580814-T
rs7085433-A
rs495828-T
rs671-A
rs12127588-A
rs4895441-G
rs6494537-C
rs6684514-A
rs1260326-C
rs3782886-G
rs671-A
rs11611647-C
rs7085433-A
rs3094212-C
rs11966072-G
rs6092477-G
rs4821112-A
rs11966072-G
rs10518733-C
rs11204538-C
rs445-T
rs12313946-C
rs7173947-C
rs2280401-A
rs9310736-A
rs2736100-G
rs7843479-A
rs470119-T
rs10495928-G
rs2544390-C
rs8176746-T		 0.35
0.28
0.35
0.43
0.39
0.27
0.27
0.44
0.38
0.12
0.28
0.12
0.31
0.28
0.19
0.24
0.17
0.46
0.26
0.26
0.15
0.28
0.26
0.21
0.37
0.27
0.21
0.44
0.27
0.26
0.37
0.15
0.35
0.10
0.42
0.47
0.10
0.40
0.16
0.32
0.47
0.29
0.16
0.26
0.40
0.29
0.21
0.17
0.49
0.18		 3 x 10-66 (MCH)
4 x 10-59 (ALP)
3 x 10-56 (MCV)
1 x 10-49 (TG)
3 x 10-26 (CK)
3 x 10-25 (MCH)
2 x 10-17 (RBC)
1 x 10-16 (AST)
4 x 10-13 (MCHC)
2 x 10-12 (PLT)
3 x 10-12 (RBC)
4 x 10-12 (MCH)
1 x 10-11 (BUN)
1 x 10-11 (Hgb)
1 x 10-10 (RBC)
2 x 10-10 (BUN)
2 x 10-10 (BUN)
3 x 10-10 (TP)
4 x 10-10 (MCH)
5 x 10-10 (MCHC)
6 x 10-10 (MCH)
6 x 10-10 (Ht)
7 x 10-10 (MCHC)
7 x 10-10 (MCH)
2 x 10-9 (WBC)
3 x 10-9 (MCH)
3 x 10-9 (MCHC)
4 x 10-9 (ALB)
5 x 10-9 (ALT)
5 x 10-9 (GGT)
6 x 10-9 (RBC)
7 x 10-9 (MCV)
7 x 10-9 (WBC)
7 x 10-9 (RBC)
1 x 10-8 (MCV)
1 x 10-8 (MCV)
1 x 10-8 (MCH)
2 x 10-8 (sCr)
2 x 10-8 (MCV)
2 x 10-8 (WBC)
3 x 10-8 (WBC)
3 x 10-8 (ALP)
3 x 10-8 (TP)
3 x 10-8 (MCV)
3 x 10-8 (RBC)
3 x 10-8 (MCV)
4 x 10-8 (MCH)
4 x 10-8 (RBC)
4 x 10-8 (urate)
4 x 10-8 (MCHC)		 2.01 [NR] % variance
3.79 [NR] % variance
1.7 [NR] % variance
2.85 [NR] % variance
1.3 [NR] % variance
.74 [NR] % variance
.49 [NR] % variance
.48 [NR] % variance
.36 [NR] % variance
.33 [NR] % variance
.33 [NR] % variance
.33 [NR] % variance
.32 [NR] % variance
.32 [NR] % variance
.29 [NR] % variance
.28 [NR] % variance
.29 [NR] % variance
.38 [NR] % variance
.27 [NR] % variance
.27 [NR] % variance
.27 [NR] % variance
.26 [NR] % variance
.26 [NR] % variance
.27 [NR] % variance
.25 [NR] % variance
.24 [NR] % variance
.24 [NR] % variance
.36 [NR] % variance
.25 [NR] % variance
.58 [NR] % variance
.23 [NR] % variance
.23 [NR] % variance
.22 [NR] % variance
.23 [NR] % variance
.22 [NR] % variance
.22 [NR] % variance
.22 [NR] % variance
.22 [NR] % variance
.22 [NR] % variance
.21 [NR] % variance
.21 [NR] % variance
.45 [NR] % variance
.3 [NR] % variance
.21 [NR] % variance
.21 [NR] % variance
.21 [NR] % variance
.21 [NR] % variance
.21 [NR] % variance
.34 [NR] % variance
.21 [NR] % variance		 Illumina
[up to 566,430]		 N
03/05/10 Cirulli
February 03, 2010
Eur J Hum Genet
Common genetic variation and performance on standardized cognitive tests. 		Cognitive test performance Up to 1,086 individuals NR 2q24.2
21q22.3
14q22.1
10p12.1
14q22.1
4q21.22
14q21.3
8q13.3
12q14.3
14q21.3
15q21.3
2p25.1
6q22.31
8q24.23
13q31.1
15q26.2
16q23.3
18q12.1
1p13.2
8q21.3
9q31.2
9q33.3
10q25.3
12q21.1
14q21.3
4q12
5p15.33
6q13
8p23.2
Xq28
15q23
2p25.3
3q13.2
5p15.33
8p23.1
8q22.3
Xq21.31
14q24.3
20q13.12
6p22.1
6q16.1
10q26.2
19p13.2
20p12.3
11q23.3
1p34.3
2q37.1
4q35.2
7q31.2
8p12		 AC092594.1
PKNOX1
ATL1, SPG3A
KIAA1217
NIN
AC067942.6-1
AL358335.4
KCNB2
TBC1D30
AL358335.4
LIPC
AC062028.1
C6orf170
FAM135B
RP11-600P1.2
MCTP2
AC009063.8
AC105245.4
RP5-965F6.2
RIPK2
TAL2
NEK6
AFAP1L2
AC131213.4
CDKL1
Intergenic
AC025187.6
RIMS1
Intergenic
IDS
RNU6-2, RNU6-1
AC079779.6
PHLDB2, PLCXD2
AC138982.2
C8orf12
NCALD
RP13-140E4.1
AC007056.4-3
RP5-995J12.2
MHC
RP11-538A16.1
RP11-264E18.1
CTC-359D24.2
PLCB1
GRIK4
RP11-109P14.2
AC010149.4
AC093909.2
AC106873.3
GTF2E2		 rs1876040-?
rs234720-?
rs17122693-?
rs2484873-?
rs8020441-?
rs7658637-?
rs7151223-?
rs2247572-?
rs939876-?
rs1584157-?
rs4775031-?
rs6739054-?
rs1343075-?
rs9657451-?
rs17070284-?
rs6496074-?
rs3784962-?
rs4145170-?
rs7555668-?
rs4397449-?
rs1463984-?
rs2807580-?
rs4751674-?
rs10879517-?
rs1265879-?
rs10517437-?
rs492478-?
rs10455248-?
rs2616984-?
rs530501-?
rs448720-?
rs4643574-?
rs4450776-?
rs17586674-?
rs2002030-?
rs517811-?
rs5941436-?
rs6574433-?
rs6017291-?
rs34704616-?
rs2506933-?
rs9804317-?
rs17638629-?
rs6118083-?
rs12797755-?
rs12117544-?
rs17275498-?
rs7659062-?
rs7782376-?
rs2978263-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 6 x 10-8 (Digit Span Backward)
2 x 10-7 (Digit Span Forward)
3 x 10-7 (Trails A)
4 x 10-7 (Digit Span Backward)
5 x 10-7 (Trails A)
6 x 10-7 (Animals)
1 x 10-6 (Digit Span Forward)
1 x 10-6 (Animals)
2 x 10-6 (Trails B)
2 x 10-6 (Digital Span Forward)
2 x 10-6 (Trails B)
2 x 10-6 (PC1)
2 x 10-6 (Immediate Story Recall)
2 x 10-6 (Delayed Story Recall)
3 x 10-6 (COWA)
3 x 10-6 (Trails B)
3 x 10-6 (Trails B)
3 x 10-6 (Animals)
3 x 10-6 (Symbol Search)
3 x 10-6 (Animals)
3 x 10-6 (Colorword)
3 x 10-6 (Digit Symbol)
4 x 10-6 (PC1)
4 x 10-6 (Trails A)
4 x 10-6 (Trails A)
4 x 10-6 (Delayed Story Recall)
4 x 10-6 (Colorword)
4 x 10-6 (Trails A)
4 x 10-6 (Digit Span Backward)
4 x 10-6 (Trails A)
5 x 10-6 (Trails B)
5 x 10-6 (Digit Span Forward)
5 x 10-6 (PC1)
5 x 10-6 (Colorword)
5 x 10-6 (Immediate Story Recall)
5 x 10-6 (Trails B)
5 x 10-6 (Trails B)
6 x 10-6 (Animals)
6 x 10-6 (Delayed Story Recall)
6 x 10-6 (Colorword)
6 x 10-6 (Animals)
7 x 10-6 (Animals)
7 x 10-6 (Trails A)
7 x 10-6 (Colorword)
8 x 10-6 (Digit Span Forward)
8 x 10-6 (Colorword)
8 x 10-6 (COWA)
8 x 10-6 (Delayed Story Recall)
8 x 10-6 (Digit Span Forward)
8 x 10-6 (Animals)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[up to 563,855]		 N
03/02/10 Shi
February 02, 2010
Mol Psychiatry
Genome-wide association study of recurrent early-onset major depressive disorder. 		Major depressive disorder 1,020 European cases, 1,636 European controls NR 18q22.1
21q21.2
1p13.3
5p13.2
2p23.2
3p14.2
1p13.3
7p15.3
13q21.33		 DSEL
Intergenic
GNAT2, GNAI3, AMPD2
GDNF
FAM179A, C2orf71
FHIT, PTPRG
ATXN7L2, SYPL2, CYB561D1
SP4
Intergenic		 rs17077540-G
rs2828520-G
rs6537837-T
rs270545-G
rs882632-T
rs10514718-C
rs12049330-G
rs17144465-G
rs9572423-G		 0.11
0.31
0.17
0.69
0.29
0.94
0.14
0.04
0.88		 2 x 10-7
4 x 10-7
1 x 10-6
1 x 10-6
2 x 10-6
4 x 10-6
6 x 10-6
6 x 10-6
9 x 10-6 		1.61
1.35
1.43
1.37
1.34
2.12
1.44
1.82
1.54 		Affymetrix
[671,424]		 N
03/05/10 Li
February 01, 2010
J Allergy Clin Immunol
Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions. 		Asthma 607 cases, 3,294 white controls NR 5q31.1
15q21.2
20p13		 RAD50
SCG3
KIAA1271		 rs2244012-C
rs17525472-?
rs4815617-?		 0.21
NR
NR		 3 x 10-7
2 x 10-6
8 x 10-6 		1.64 [1.36-1.97]
NR
NR		 Illumina
[292,443]		 N
03/12/10 Karasik
January 29, 2010
J Bone Miner Res
Genome-wide pleiotropy of osteoporosis-related phenotypes: The Framingham study. 		Osteoporosis-related phenotypes 2,073 related women NR 2q36.1 SCG2 rs16864755-? 4 x 10-6 (Femoral Neck BMD) .24 [0.14-0.34] cm3 increase Affymetrix
[433,510]		 N
02/28/10 Petersen
January 24, 2010
Nat Genet
A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33. 		Pancreatic cancer 3,851 cases, 3,934 controls NR 13q22.1
1q32.1
5p15.33		 KLF5, KLF12
NR5A2
CLPTM1L		 rs9543325-C
rs3790844-T
rs401681-T		 0.37
0.76
0.45		 3 x 10-11
2 x 10-10
7 x 10-7 		1.26 [1.18-1.35]
1.3 [1.19-1.41]
1.19 [1.11-1.27]		 Illumina
[551,766]		 N
02/12/10 Shen
January 22, 2010
Neuroimage
Whole Genome Association Study of Brain-Wide Imaging Phenotypes for Identifying Quantitative Trait Loci in MCI and AD: A Study of the ADNI Cohort 		Brain imaging 175 Caucasian Alzheimer patients, 354 Caucasian amnestic mild cognitive impairment patients, 204 Caucasian controls NR 10q21.1
19q13.32
19q13.32
1p31.3
2q36.1
3p14.1
3q28
4p15.1
7p21.3
7q35		 UBE2D1
TOMM40
APOE
LOC199897
EPHA4
LOC642487
TP63
LOC391642
NXPH1
LOC643308		 rs16912145-?
rs2075650-?
rs429358-?
rs7526034-?
rs10932886-?
rs7647307-?
rs7610017-?
rs4692256-?
rs6463843-?
rs12531488-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10- (RHippocampus)
x 10 <1 x 10-6 (multiple phenotypes)
x 10 <1 x 10-6 (multiple phenotypes)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[530,992]		 N
02/10/10 Kung
January 20, 2010
Am J Hum Genet
Association of JAG1 with bone mineral density and osteoporotic fractures: a genome-wide association study and follow-up replication studies. 		Bone mineral density 785 Hong Kong Southern Chinese (HSKC) extreme BMD females 720 HKSC extreme BMD individuals, 17,378 individuals of European or Asian descent 20p12.2 JAG1 rs2273061-A 0.31 5 x 10-8 (lumbar spine) .07 [NR] s.d. increase Illumina
[488,853]		 N
02/28/10 Dupuis
January 17, 2010
Nat Genet
New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. 		Fasting glucose-related traits up to 46,186 European descent individuals up to 76,558 European ancestry individuals 11q14.3
2q31.1
7p13
2q31.1
7p21.2
11q14.3
2p23.3
2p23.3
3q21.1
2p23.3
11p11.2
7p21.2
7p13
10q25.2
11q12.2
11p11.2
9p24.2
11q12.2
3q26.2
9p24.2
3q21.1
1q32.3
8q24.11
12q23.2
10q25.2
12q23.2
15q22.2
10q25.2
1q32.3
3q26.2		 MTNR1B
G6PC2
GCK
G6PC2
DGKB, TMEM195
MTNR1B
GCKR
GCKR
ADCY5
GCKR
MADD
DGKB, TMEM195
GCK
ADRA2A
FADS1
CRY2
GLIS3
FADS1
SLC2A2
GLIS3
ADCY5
PROX1
SLC30A8
IGF1
TCF7L2
IGF1
C2CD4B
ADRA2A
PROX1
SLC2A2		 rs10830963-G
rs560887-C
rs4607517-A
rs560887-C
rs2191349-T
rs10830963-G
rs780094-C
rs780094-C
rs11708067-A
rs780094-C
rs7944584-A
rs2191349-T
rs4607517-A
rs10885122-G
rs174550-T
rs11605924-A
rs7034200-A
rs174550-T
rs11920090-T
rs7034200-A
rs11708067-A
rs340874-C
rs11558471-A
rs35767-G
rs4506565-T
rs35767-G
rs11071657-A
rs10885122-G
rs340874-C
rs11920090-T		 0.30
0.70
0.16
0.70
0.52
0.30
0.62
0.62
0.78
0.62
0.75
0.52
0.16
0.87
0.64
0.49
0.49
0.64
0.87
0.49
0.78
0.52
0.31
0.85
0.31
0.85
0.63
0.87
0.52
0.87		 6 x 10-175 (FPG)
9 x 10-218 (FPG)
7 x 10-92 (FPG)
2 x 10-66 (HOMA-B)
3 x 10-44 (FPG)
3 x 10-43 (HOMA-B)
6 x 10-38 (FPG)
3 x 10-24 (HOMA-IR)
7 x 10-22 (FPG)
4 x 10-20 (FI)
2 x 10-18 (FPG)
3 x 10-17 (HOMA-B)
2 x 10-16 (HOMA-B)
3 x 10-16 (FPG)
2 x 10-15 (FPG)
1 x 10-14 (FPG)
1 x 10-13 (HOMA-B)
5 x 10-13 (HOMA-B)
8 x 10-13 (FPG)
1 x 10-12 (FPG)
3 x 10-12 (HOMA-B)
7 x 10-12 (FPG)
3 x 10-11 (FPG)
2 x 10-9 (HOMA-IR)
1 x 10-8 (FPG)
3 x 10-8 (FI)
4 x 10-8 (FPG)
2 x 10-6 (HOMA-B)
5 x 10-6 (HOMA-B)
5 x 10-6 (HOMA-B)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
02/28/10 " Fasting insulin-related traits up to 46,186 European descent individuals up to 76,558 European ancestry individuals 2p23.3
2p23.3
12q23.2
12q23.2		 GCKR
GCKR
IGF1
IGF1		 rs780094-C
rs780094-C
rs35767-G
rs35767-G		 0.62
0.62
0.85
0.85		 3 x 10-24 (HOMA-IR)
4 x 10-20 (FI)
2 x 10-9 (HOMA-IR)
3 x 10-8 (FI)		 NR
NR
NR
NR		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
02/08/10 McMahon
January 17, 2010
Nat Genet
Meta-analysis of genome-wide association data identifies a risk locus for major mood disorders on 3p21.1. 		Major mood disorders 6,686 European cases, 9,068 European controls 1,930 European cases, 2,747 European controls 3p21.1 PBRM1 rs2251219-? 0.59 2 x 10-9 1.14 [1.09-1.18] Affymetrix, Illumina and Perlegen
[~2.1 million] (imputed)		 N
02/08/10 Saxena
January 17, 2010
Nat Genet
Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge. 		Two-hour glucose challenge 15,234 European individuals up to 30,620 European individuals 3q21.1
19q13.32
2p23.3
10q25.2
15q22.2		 ADCY5
GIPR
GCKR
TCF7L2
VPS13C		 rs2877716-C
rs10423928-A
rs1260326-T
rs12243326-C
rs17271305-G		 NR
NR
NR
NR
NR		 7 x 10-16
3 x 10-12
3 x 10-10
1 x 10-7
1 x 10-7 		.09 [0.07-0.11] mmol/L increase
.09 [0.07-0.11] mmol/L increase
.07 [0.05-0.09] mmol/L increase
.08 [0.06-0.10] mmol/L increase
.06 [0.04-0.08 mmol/L increase		 Affymetrix & Illumina
[NR]		 N
02/05/10 Edwards
January 13, 2010
Ann Hum Genet
Genome-wide association study confirms SNPs in SNCA and the MAPT region as common risk factors for Parkinson disease. 		Parkinson's disease 1,752 Caucasian cases, 1,745 Caucasian controls NR 17q21.31
4q22.1
1p36.13
9q33.1
4p16.3
5q35.3		 PLEKHM1, MAPT, IMP5
SNCA
TAS1R2
DBC1
DGKQ
NR		 rs11012-T
rs2736990-?
rs12063142-?
rs4837628-A
rs11248060-?
rs10464059-A		 NR
NR
NR
NR
NR
NR		 6 x 10-8
7 x 10-8
5 x 10-7
1 x 10-6
2 x 10-6
3 x 10-6 		1.43 [1.27-1.61]
1.29 [1.18-1.43]
NR
1.27 [1.15-1.39]
NR
1.33 [1.19-1.52]		 Illumina
[495,715] (imputed)		 N
02/04/10 Van Laer
January 13, 2010
Eur J Hum Genet
A genome-wide association study for age-related hearing impairment in the Saami. 		Hearing impairment 347 Finnish Saami individuals NR 5q13.3
6q22.33		 IQGAP2
NR		 rs457717-T
rs10499138-A		 0.25
0.25		 4 x 10-7 (PC3)
2 x 10-6 (PC2)		 NR
NR		 Affymetrix
[83,381]		 N
02/02/10 Chung
January 12, 2010
Pharmacogenomics J
A genome-wide association study identifies new loci for ACE activity: potential implications for response to ACE inhibitor. 		Angiotensin-converting enzyme activity 400 Han Chinese hypertensives 623 Han Chinese hypertensives 17q23.3
9q34.2		 ACE
ABO		 rs4343-G
rs495828-A		 0.31
0.17		 3 x 10-25
3 x 10-8 		16.2 [NR] % variance
4.9 [NR] % variance		 Illumina
[~550,000]		 N
01/29/10 Chambers
January 10, 2010
Nat Genet
Genetic variation in SCN10A influences cardiac conduction. 		Electrocardiographic traits 6,543 Indian Asians 6,243 Indian Asians, 5,370 Europeans 3p22.2
1q23.3
7q36.1		 SCN10A
NOS1AP
KCNH2		 rs6795970-A
rs1415259-A
rs4725982-A		 0.36
0.39
NR		 3 x 10-15 (PR interval)
7 x 10-10 (QTc interval)
3 x 10-6 (QTc interval)		 3.33 [2.51-4.15] ms increase
2.53 [1.73-3.33] ms decrease
2.08 [1.20-2.96] ms increase		 Illumina
[303,309]		 N
01/21/10 Crowther-Swanepoel
January 10, 2010
Nat Genet
Common variants at 2q37.3, 8q24.21, 15q21.3 and 16q24.1 influence chronic lymphocytic leukemia risk. 		Chronic lymphocytic leukemia 505 European cases, 1,438 European controls 1,998 European cases, 4,351 European controls 8q24.21
2q37.3
16q24.1
19q13.32
15q21.3
18q21.1
15q25.2		 Intergenic
FARP2
IRF8
NR
NEDD4, RFX7
CXXC1, MBD1
CPEB1		 rs2456449-G
rs757978-A
rs305061-T
rs11668878-T
rs7169431-A
rs1036935-T
rs783540-G		 NR
NR
NR
NR
NR
NR
NR		 8 x 10-10
2 x 10-9
4 x 10-7
4 x 10-7
5 x 10-7
2 x 10-6
4 x 10-6 		1.26 [1.17-1.35]
1.38 [1.25-1.56]
1.22 [1.12-1.32]
1.37 [1.21-1.55]
1.36 [1.21-1.53]
1.22 [1.12-1.32]
1.18 [1.10-1.27]		 Illumina
[299,983]		 N
02/02/10 Holm
January 10, 2010
Nat Genet
Several common variants modulate heart rate, PR interval and QRS duration. 		Electrocardiographic traits Up to 12,670 Icelandic individuals Up to 10,352 Icelandic individuals 3p22.2
1q23.3
4q21.23
12q24.21
7q31.2
21q22.12
12q24.21
7q36.1
11p15.5
14q11.2
6p21.2
3p22.2
3p22.2
10q21.1
12q24.21
3p22.2
6p22.31
16q21		 SCN10A
NOS1AP
ARHGAP24
TBX5
CAV1
KCNE1
TBX5
KCNH2
KCNQ1
MYH6
CDKN1A
SCN5A
SCN10A
DKK1
TBX5
SCN5A
C6orf204
NDRG4		 rs6795970-A
rs10494366-G
rs7660702-T
rs3825214-G
rs3807989-A
rs727957-T
rs3825214-G
rs3807375-T
rs12296050-T
rs365990-G
rs1321311-T
rs11129795-G
rs6795970-A
rs1733724-T
rs3825214-G
rs12053903-T
rs11970286-T
rs37062-A		 0.36
0.39
0.74
0.22
0.40
0.19
0.22
0.35
0.15
0.34
0.21
0.77
0.36
0.21
0.22
0.72
0.54
0.72		 1 x 10-58 (PR interval)
5 x 10-22 (QT interval)
3 x 10-17 (PR interval)
3 x 10-13 (QRS duration)
7 x 10-13 (PR interval)
2 x 10-12 (QT interval)
3 x 10-12 (PR interval)
5 x 10-11 (QT interval)
8 x 10-11 (QT interval)
9 x 10-11 (HR)
3 x 10-10 (QRS duration)
5 x 10-10 (QRS complex)
4 x 10-9 (QRS duration)
7 x 10-8 (QRS duration)
1 x 10-7 (QT interval)
1 x 10-7 (PR interval)
8 x 10-7 (QT interval)
1 x 10-6 (QT interval)		 14.81 [13.01-16.60] % s.d. increase
12.2 [9.72-14.68] % s.d. increase
8.46 [6.50-10.42] % s.d. increase
7.35 [5.37-9.33] % s.d. increase
6.4 [4.65-8.15] % s.d. increase
11.7 [8.46-14.94] % s.d. increase
7.36 [5.29-9.43] % s.d. increase
11.95 [8.39-15.51] % s.d. increase
13.16 [9.19-17.12] % s.d. increase
5.25 [3.66-6.83] % s.d. increase
6.52 [4.50-8.55] % s.d. increase
8.24 [5.64-10.83] % s.d. decrease
5.17 [3.46-6.89] % s.d. increase
5.62 [3.58-7.66] % s.d. increase
5.88 [3.72-8.03] % s.d. increase
6.59 [4.16-9.03] % s.d. decrease
6.19 [3.73-8.65] % s.d. increase
6.09 [3.62-8.57] % s.d. increase		 Illumina
[306,060]		 N
02/04/10 Pfeufer
January 10, 2010
Nat Genet
Genome-wide association study of PR interval. 		PR interval 28,517 European descent individuals NR 3p22.2
7q31.2
3p22.2
4q21.23
12q24.21
12p12.1
5q35.1
2p14
11q13.5		 SCN10A
CAV1, CAV2
SCN5A
ARHGAP24
TBX5, TBX3
SOX5, C12orf67
NKX2-5, C5orf41
MEIS1
WNT11		 rs6800541-C
rs3807989-A
rs11708996-C
rs7692808-A
rs1896312-C
rs11047543-A
rs251253-C
rs11897119-C
rs4944092-G		 0.40
0.40
0.15
0.31
0.28
0.15
0.40
0.39
0.32		 2 x 10-74
4 x 10-28
6 x 10-26
6 x 10-20
3 x 10-17
3 x 10-13
9 x 10-13
5 x 10-11
3 x 10-8 		3.77 [3.37-4.17] ms increase
2.3 [1.89-2.71] ms increase
3.04 [2.47-3.61] ms increase
2.01 [1.58-2.44] ms decrease
1.95 [1.50-2.40] ms increase
2.09 [1.53-2.65] ms decrease
1.49 [1.08-1.90] ms decrease
1.36 [0.95-1.77] ms increase
1.19 [0.77-1.61] ms decrease		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
02/02/10 The Australo-Anglo-American Spondyloarthritis Consortium (TASC)
January 10, 2010
Nat Genet
Genome-wide association study of ankylosing spondylitis identifies non-MHC susceptibility loci. 		Ankylosing spondylitis 2,053 European descent cases, 5,140 European descent controls 898 British cases, 1,518 British controls 6p21.33
21q22.2
2p15
1p31.3
5q15
4q21.21
2q11.2
2q31.3
10p12.31		 MHC
PSMG1
B3GNT2
IL23R
ERAP1
ANTXR2
IL1R2
NR
NR		 rs7743761-?
rs2242944-?
rs10865331-A
rs11209026-?
rs27434-A
rs4333130-?
rs2310173-A
rs1018326-C
rs1326986-C		 NR
0.63
0.40
0.94
0.23
0.64
0.45
0.45
0.05		 5 x 10-304
8 x 10-20
2 x 10-19
9 x 10-14
5 x 10-12
9 x 10-8
5 x 10-7
2 x 10-6
4 x 10-6 		NR
1.39 [1.28-1.49]
1.27 [1.18-1.37]
1.89 [1.56-2.27]
1.19 [1.10-1.30]
1.22 [1.12-1.32]
1.18 [1.10-1.27]
1.24 [1.15-1.33]
1.9 [1.58-2.29]		 Illumina
[288,662]		 N
01/28/10 Guo
January 08, 2010
PLoS Genet
Genome-wide association study identifies ALDH7A1 as a novel susceptibility gene for osteoporosis. 		Osteoporosis 350 Han Chinese cases, 350 Han Chinese controls 390 Han Chinese cases, 516 Han Chinsese controls 5q23.2 ALDH7A1 rs13182402-G 0.05 2 x 10-9 2.25 [1.72-2.94] Affymetrix
[281,533]		 N
01/21/10 Igl
January 08, 2010
PLoS Genet
Modeling of environmental effects in genome-wide association studies identifies SLC2A2 and HP as novel loci influencing serum cholesterol levels. 		Cholesterol 656 Swedish individuals Up to 3,996 European individuals 16q13 CETP rs1532624-? NR 3 x 10-20 9.99 [NR] mg/dl increase between hmz Illumina
[~311,388]		 N
02/28/10 Kerkhof
January 07, 2010
Arthritis Rheum
A genome-wide association study identifies an osteoarthritis susceptibility locus on chromosome 7q22. 		Osteoarthritis 1,341 European cases, 3,496 European controls 13,597 European cases, up to 40,000 European controls 7q22.3 COG5 rs3815148-C 0.23 8 x 10-8 1.14 [1.09-1.19] Illumina
[500,510]		 N
01/21/10 Rauch
January 07, 2010
Gastroenterology
Genetic variation in IL28B Is Associated with Chronic Hepatitis C and Treatment Failure - A Genome-Wide Association Study 		Chronic Hepatitis C infection 1,015 Swiss chronic HCV patients, 347 Swiss spontaneously cleared HCV patients NR 19q13.3 IL28B, IL28A, IL29 rs8099917-G 0.24 6 x 10-9 2.31 [1.74-3.06] Illumina
[~500,000]		 N
03/17/10 Liu
January 01, 2010
J Am Acad Child Adolesc Psychiatry
A genome-wide association study of amygdala activation in youths with and without bipolar disorder. 		Functional MRI 39 adolescents with bipolar disease, 29 unaffected adolescents NR 20q13.2
19q13.11		 DOK5
KIAA0355		 rs2023454-?
rs10407640-?		 NR
NR		 5 x 10-7 (hostility, right amygdala)
7 x 10-6 (hostility, left amygdala)		 .22 [NR] % variance explained
.31 [NR] % variance explained		 Illumina
[104,043]		 N
01/19/10 Shrestha
January 01, 2010
AIDS
A genome-wide association study of carotid atherosclerosis in HIV-infected men. 		Carotid atherosclerosis in HIV infection 177 Caucasian HIV-infected men NR 15q14
7q31.33
7p15.2
22q12.2
5q12.3
10q23.1
5q34		 RYR3
GRM8
Intergenic
RFPL1, AP1B1, THOC5, NF2
MAST4
Intergenic
Intergenic		 rs2229116-G
rs17691394-G
rs17151904-A
rs13053817-A
rs1697137-C
rs588517-A
rs958994-G		 0.18
0.20
0.20
0.18
0.36
0.15
0.27		 3 x 10-8 (common cIMT)
9 x 10-7 (common cIMT)
1 x 10-6 (internal cIMT)
2 x 10-6 (common cIMT)
2 x 10-6 (internal cIMT)
8 x 10-6 (internal cIMT)
8 x 10-6 (common cIMT)		 NR
NR
NR
NR
NR
NR
NR		 Illumina
[311,194]		 N
01/19/10 Debette
December 31, 2009
Stroke
Genome-Wide Association Studies of MRI-Defined Brain Infarcts. Meta-Analysis From the CHARGE Consortium 		Subclinical brain infarct 9,401 white individuals 1,822 white individuals, 644 black individuals NS NS NS NS NS NS Affymetrix & Illumina
[2,217,889] (imputed)		 N
01/19/10 Papassotiropoulos
December 29, 2009
Mol Psychiatry
A genome-wide survey of human short-term memory 		Memory (short-term) 333 young Swiss individuals 777 young European individuals, 922 elderly German individuals NS NS NS NS NS NS Affymetrix
[841,663]		 N
01/19/10 Shyn
December 29, 2009
Mol Psychiatry
Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies. 		Major depressive disorder (broad) 3,957 cases, 3,428 controls NR 8p21.3
7p15.3
3p26.1
7q32.3
2p14
3q26.32
Xq21.33
10p12.1
6p25.1		 ATP6V1B2, SLC18A1, LZTS1
SP4
GRM7
AK294384
BC043421
NR
NR
NR
LY86		 rs1106634-A
rs17144465-G
rs9870680-T
rs10265216-A
rs724568-C
rs644695-A
rs5990417-T
rs1612122-T
rs2326810-G		 0.14
0.03
0.44
0.28
0.36
0.88
0.83
0.48
0.92		 7 x 10-7
8 x 10-7
1 x 10-6
3 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6 		1.3 [NR]
1.56 [NR]
1.19 [NR]
1.19 [NR]
1.17 [NR]
1.35 [NR]
1.23 [NR]
1.17 [NR]
1.41 [NR]		 Affymetrix and Perlegen
[2,391,203] (imputed)		 N
01/13/10 Illig
December 27, 2009
Nat Genet
A genome-wide perspective of genetic variation in human metabolism. 		Serum metabolites 1,809 European individuals 422 European females 11q12.2
12q24.31
1p31.1
2q34
4q32.1		 FADS1
ACADS
ACADM
ACADL
ETFDH		 rs174547-C
rs2014355-T
rs211718-C
rs2286963-T
rs8396-T		 0.30
0.28
0.31
0.37
0.30		 7 x 10-179 (PC aa C36:3/PC aa C36:4)
5 x 10-96 (C3/C4)
1 x 10-63 (C12/C10)
3 x 10-60 (C9/C10:2)
4 x 10-24 (C14:1-OH/C10)		 36.3 [NR] % variance explained
21.5 [NR] % variance explained
14.6 [NR] % variance explained
13.8 [NR] % variance explained
5.6 [NR] % variance explained		 Illumina
[517,480]		 N
01/19/10 Fellay
December 24, 2009
PLoS Genet
Common genetic variation and the control of HIV-1 in humans. 		HIV-1 control 2,362 Caucasian cases NR 6p21.33
6p21.33
6p21.33
6p21.33
6p22.1
4q32.1
6p21.33
14q23.1
6q24.3
7p21.1
6p21.33
6p12.1
Xq26.2
11q14.3
6p22.1
11q14.3
13q13.3
2q37.1
16q23.1
1q21.1
2p16.1
6p21.33
6p22.1
10q11.23
6p21.32
6q27
10q26.2
6p21.33
2q32.3
3p23
1q42.3
2p25.2
18q21.31
5q32
8q13.3
9q21.13
Xq21.31
16p13.2
2q22.3
1p32.2
21q22.12
5q23.2		 HCP5, HLA-B
HLA-C
HLA-C
HCP5, HLA-B
ZNRD1, RNF39, HLA-A
Intergenic
SNORD52
Intergenic
Intergenic
Intergenic
CDSN
HCRTR2
Intergenic
Intergenic
C6orf12, ZNRD1
Intergenic
Intergenic
Intergenic
Intergenic
NR
Intergenic
DDR1, VARS2, DPCR1
TRIM10
Intergenic
BTNL2, NOTCH4
NR
Intergenic
TNXB
Intergenic
Intergenic
Intergenic
NR
Intergenic
NR
NR
Intergenic
Intergenic
NR
Intergenic
NR
NR
Intergenic		 rs2395029-G
rs9264942-C
rs9264942-?
rs2395029-?
rs7758512-?
rs17291045-?
rs9368699-?
rs8013190-?
rs9497975-?
rs38152-?
rs3815087-?
rs9367630-?
rs17324272-?
rs16914280-?
rs259919-?
rs12274302-?
rs1777672-?
rs13394720-?
rs16948255-?
rs12122100-?
rs6751715-?
rs7756521-?
rs9468692-?
rs4838508-?
rs3763313-?
rs3734905-?
rs11818629-?
rs12198173-?
rs1385351-?
rs17027625-?
rs2069084-?
rs1405262-?
rs1120787-?
rs2304069-?
rs16936455-?
rs11143609-?
rs12012519-?
rs1463132-?
rs10928302-?
rs10159302-?
rs2834812-?
rs2637496-?		 0.048
0.412
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 5 x 10-35 (setpoint)
6 x 10-32 (setpoint)
6 x 10-12 (progression)
1 x 10-11 (progression)
2 x 10-8 (progression)
5 x 10-8 (progression)
5 x 10-8 (progression)
7 x 10-8 (progression)
7 x 10-8 (progression)
7 x 10-8 (progression)
8 x 10-8 (progression)
1 x 10-7 (progression)
2 x 10-7 (progression)
3 x 10-7 (progression)
3 x 10-7 (setpoint)
4 x 10-7 (progression)
4 x 10-7 (progression)
5 x 10-7 (progression)
1 x 10-6 (progression)
1 x 10-6 (progression)
1 x 10-6 (progression)
1 x 10-6 (progression)
1 x 10-6 (setpoint)
2 x 10-6 (progression)
2 x 10-6 (progression)
2 x 10-6 (progression)
3 x 10-6 (progression)
3 x 10-6 (progression)
4 x 10-6 (progression)
4 x 10-6 (progression)
6 x 10-6 (progression)
6 x 10-6 (progression)
7 x 10-6 (progression)
7 x 10-6 (progression)
7 x 10-6 (progression)
7 x 10-6 (progression)
7 x 10-6 (progression)
8 x 10-6 (progression)
8 x 10-6 (progression)
9 x 10-6 (progression)
9 x 10-6 (progression)
9 x 10-6 (progression)		 5.8 [NR] % increase
5.3 [NR] % increase
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[NR]		 N
01/13/10 Sleiman
December 23, 2009
N Engl J Med
Variants of DENND1B associated with asthma in children. 		Asthma 793 European ancestry child cases, 1,988 European ancestry child controls 917 European ancestry child cases, 1,546 European ancestry child controls, 1,667 African American child cases, 2,045 African American child controls 1q31.3 DENND1B, CRB1 rs2786098-? 0.85 2 x 10-13 1.43 [NR] (European ancestry) Illumina
[~550,000]		 N
12/28/09 Mangold
December 20, 2009
Nat Genet
Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. 		Nonsyndromic cleft lip with or without cleft palate 399 European origin cases, 1,318 European origin controls 739 European origin triads 17q22
10q25.3
2p21
13q31.1
15q13.3
17q22		 NOG
KIAA1598, VAX1
THADA
SPRY2
FMN1, GREM1
NOG		 rs227731-C
rs7078160-A
rs7590268-G
rs9574565-C
rs1258763-A
rs17760296-G		 0.42
0.16
0.22
0.74
0.66
0.16		 1 x 10-8
2 x 10-8
9 x 10-8
3 x 10-7
1 x 10-6
7 x 10-6 		1.38 [1.21-1.56]
1.36 [1.21-1.53]
1.42 [1.26-1.59]
1.31 [1.01-1.70]
1.52 [1.23-1.86]
1.5 [1.32-1.69]		 Illumina
[521,288]		 N
12/28/09 Zhang
December 16, 2009
N Engl J Med
Genomewide association study of leprosy. 		Leprosy 706 Han Chinese cases, 1,225 Han Chinese controls 3,254 Chinese cases, 5,955 Chinese controls 13q14.11
16q12.1
6p21.32
9q32
8q21.3
8q21.3		 C13orf31
NOD2
HLA-DR-DQ
TNFSF15
RIPK2
RIPK2		 rs3764147-G
rs9302752-G
rs602875-A
rs6478108-A
rs42490-G
rs40457-A		 0.31
0.29
0.68
0.46
0.58
0.28		 4 x 10-54
4 x 10-40
5 x 10-27
3 x 10-21
1 x 10-16
1 x 10-12 		1.68 [1.57-1.80]
1.59 [1.49-1.71]
1.61 [1.39-1.61]
1.37 [1.28-1.46]
1.32 [1.23-1.41]
1.3 [1.20-1.39]		 Illumina
[491,883]		 N
01/13/10 Hancock
December 13, 2009
Nat Genet
Meta-analyses of genome-wide association studies identify multiple loci associated with pulmonary function. 		Pulmonary function 20,890 European ancestry individuals 16,178 European ancestry individuals 4q31.21
4q24
6p21.32
5q32
5q33.3
6q24.1
4q22.1
9q22.32		 HHIP
INTS12, NPNT, FLJ20184, GSTCD
AGER, PPT2
HTR4
ADAM19
GPR126
FAM13A
PTCH1		 rs1980057-T
rs11727189-T
rs2070600-T
rs11168048-T
rs2277027-A
rs3817928-A
rs2869967-T
rs16909898-A		 0.40
0.06
0.04
0.58
0.71
0.78
0.61
0.90		 3 x 10-20 (FEV1/FVC)
5 x 10-17 (FEV1)
3 x 10-14 (FEV1/FVC)
1 x 10-11 (FEV1/FVC)
1 x 10-10 (FEV1/FVC)
1 x 10-9 (FEV1/FVC)
1 x 10-7 (FEV1/FVC)
5 x 10-7 (FEV1/FVC)		 .52 [NR] % increase
64.7 [NR] ml increase
1 [NR] % increase
.4 [NR] % decrease
.38 [NR] % increase
.42 [NR] % decrease
.3 [NR] % increase
.5 [NR] % increase		 Affymetrix & Illumina
[2,534,500] (imputed)		 N
12/28/09 Repapi
December 13, 2009
Nat Genet
Genome-wide association study identifies five loci associated with lung function. 		Pulmonary function 20,288 European ancestry individuals up to 54,276 European ancestry individuals 4q24
6p21.32
15q23
4q31.22
2q35
5q33.1
6p21.2		 GSTCD
AGER
THSD4
HHIP
TNS1
HTR4
DAAM2		 rs10516526-G
rs2070600-T
rs12899618-G
rs12504628-T
rs2571445-G
rs3995090-C
rs2395730-C		 0.06
0.06
0.85
0.56
0.60
0.41
0.42		 2 x 10-23 (FEV1)
3 x 10-15 (FEV1/FVC)
7 x 10-15 (FEV1/FVC)
6 x 10-13 (FEV1/FVC)
1 x 10-12 (FEV1)
4 x 10-9 (FEV1)
8 x 10-8 (FEV1/FVC)		 .14 [NR] % variance explained
.09 [NR] % variance explained
.09 [NR] % variance explained
.27 [NR] % variance explained
.07 [NR] % variance explained
.07 [NR] % variance explained
.07 [NR] % variance explained		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
01/08/10 Ronald
December 13, 2009
Behav Genet
A Genome-Wide Association Study of Social and Non-Social Autistic-Like Traits in the General Population Using Pooled DNA, 500 K SNP Microarrays and Both Community and Diagnosed Autism Replication Samples 		Social and Non-Social Autistic-Like Traits Up to 870 European boys (low and high extremes) 3,494 European children NS NS NS NS NS NS Affymetrix
[up to 435,457] (pooled)		 N
03/22/10 Zhao
December 11, 2009
J Bone Miner Res
Genome-wide association study for femoral neck bone geometry 		Femoral neck bone geometry 987 Caucasian individuals 1,488 Caucasian individuals, 2,118 Chinese individuals NS NS NS NS NS NS Affymetrix
[379,319]		 N
12/28/09 Castro-Giner
December 06, 2009
BMC Med Genet
A pooling-based genome-wide analysis identifies new potential candidate genes for atopy in the European Community Respiratory Health Survey (ECRHS). 		Atopy 75 European atopy and asthma cases, 75 European atopy only cases, 75 European controls 429 European atopy cases, 222 European controls 2p21 SGK493 rs4952590-? 0.86 2 x 10-6 1.92 [1.27-2.86] Illumina
[NR] (pooled)		 N
12/28/09 Wallace
December 06, 2009
Nat Genet
The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes. 		Type 1 diabetes 7,514 European ancestry cases, 9,045 European ancestry controls 4,840 European ancestry cases, 2,670 European ancestry controls, 4,152 European ancestry familial triads 14q32.2
19p13.2		 DLK1, MEG3, RTL1, DIO3
TYK2		 rs941576-A
rs2304256-C		 0.57
0.71		 1 x 10-10
4 x 10-9 		1.11 [1.06-1.16]
1.16 [1.11-1.22]		 Affymetrix & Illumina
[~2.6 million](imputed)		 N
01/07/10 Richards
December 05, 2009
PLoS Genet
A genome-wide association study reveals variants in ARL15 that influence adiponectin levels. 		Adiponectin levels 8,531 European ancestry individuals 6,202 European descent individuals 3q27.3
3q27.3
5q11.2		 ADIPOQ
ADIPOQ
ARL15		 rs266717-C
rs1648707-C
rs4311394-G		 0.48
0.07
0.41		 9 x 10-19
3 x 10-12
3 x 10-8 		1.07 [NR] ug/ml increase
.94 [NR] ug/ml increase
.96 [NR] ug/ml increase		 Affymetrix & Illumina
[~2.2 million] (imputed)		 N
01/13/10 Heid
December 02, 2009
Atherosclerosis
Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals. 		Adiponectin levels 4,659 European individuals 13,795 European descent individuals 3q27.3 ADIPOQ rs17366568-G 0.89 1 x 10-41 .13 [NR] log(ug/ml) increase Affymetrix and Illumina
[2,585,854] (imputed)		 N
12/28/09 Zhou
November 30, 2009
Arthritis Rheum
HLA-DPB1 and DPB2 are genetic loci for systemic sclerosis: A genome-wide association study in Koreans with replication in North Americans 		Systemic sclerosis 133 Korean cases, 557 Korean controls 1,107 Caucasian cases, 2,747 Caucasian controls NS NS NS NS NS NS Affymetrix
[440,734]		 N
12/18/09 Karlsen
November 25, 2009
Gastroenterology
Genome-wide association analysis in primary sclerosing cholangitis 		Primary sclerosing cholangitis 285 Norwegian cases, 298 Norwegian controls 766 European cases, 2,935 European controls NS NS NS NS NS NS Affymetrix
[375,487]		 N
12/28/09 Nuinoon
November 19, 2009
Hum Genet
A genome-wide association identified the common genetic variants influence disease severity in beta(0)-thalassemia/hemoglobin E. 		Beta thalassemia/hemoglobin E disease 235 mild Thai-Chinese cases, 383 severe Thai-Chinese cases 52 mild Indonesian cases, 122 severe Indonesian cases 11p15.4
6q23.3
2p16.1		 HBE1, HBG2, HBG1, HBD, HBBP1
HBS1L, MYB
BCL11A		 rs2071348-?
rs9376092-?
rs766432-?		 0.50
0.23
0.24		 3 x 10-15
2 x 10-11
1 x 10-10 		4.05 [2.64-6.21]
2.91 [2.12-3.99]
2.8 [2.04-3.84]		 Illumina
[548,094]		 N
12/14/09 Asano
November 15, 2009
Nat Genet
A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. 		Ulcerative colitis 376 Japanese cases, 934 Japanese controls 376 Japanese cases, 1,097 Japanese controls 6p21.33
6p21.32
1q23.3
13q12.13
7q31.1
9p24.1
6p21.32		 HLA
Intergenic
FCGR2A
USP12
SLC26A3
JAK2, INSL6, INSL4
BTNL2		 rs9263739-T
rs2395185-G
rs1801274-?
rs17085007-C
rs2108225-A
rs10975003-C
rs9268480-G		 0.15
0.61
0.78
0.23
0.65
0.19
0.91		 4 x 10-67
5 x 10-22
2 x 10-12
7 x 10-8
1 x 10-7
1 x 10-6
3 x 10-6 		2.73 [2.43-3.07]
1.92 [1.68-2.19]
1.59 [1.39-1.82]
1.35 [1.21-1.51]
1.32 [1.19-1.47]
1.34 [1.18-1.51]
1.82 [1.43-2.33]		 Illumina
[513,923]		 N
12/11/09 Barrett
November 15, 2009
Nat Genet
Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. 		Ulcerative colitis 2,361 European ancestry cases, 5,417 European ancestry controls 2,321 European ancestry cases, 4,818 European ancestry controls 6p21.32
20q13.12
1p36.13
1p31.3
3p21.31
16q22.1
7q31.1
1q32.1
10q24.2
13q14.11
1p36.12
1q32.1
9q34.3		 MHC
HNF4A
OTUD3, PLA2G2E
IL23R
MST1
CDH1
LAMB1
IL10
NKX2, NKX3
Intergenic
Intergenic
KIF21B
CARD9		 rs9268877-?
rs6017342-C
rs6426833-?
rs11209026-?
rs9858542-?
rs1728785-G
rs886774-G
rs3024493-?
rs6584283-?
rs9548988-T
rs7524102-A
rs7554511-?
rs10781500-?		 NR
0.52
NR
NR
NR
0.76
0.41
NR
NR
0.46
0.83
NR
NR		 4 x 10-23
9 x 10-17
2 x 10-11
3 x 10-10
7 x 10-9
3 x 10-8
3 x 10-8
8 x 10-8
2 x 10-7
3 x 10-7
3 x 10-7
1 x 10-6
7 x 10-6 		NR
1.17 [1.09-1.26]
NR
NR
NR
1.17 [1.07-1.27]
1.11 [1.03-1.19]
NR
NR
1.1 [1.03-1.19]
1.1 [1.00-1.21]
NR
NR		 Affymetrix
[NR]		 N
12/10/09 Imielinski
November 15, 2009
Nat Genet
Common variants at five new loci associated with early-onset inflammatory bowel disease. 		Inflammatory bowel disease (early onset) 2,413 European ancestry cases, 6,158 European ancestry controls 1,013 European ancestry cases, 5,805 European ancestry controls 19q13.11
16p11.2
22q12.2
10q22.3		 Intergenic
IL27, CCDC101, CLN3, EIF3C, NUPR1, SULT1A1, SULT1A2
HORMAD2, MTMR3, LIF
ZMIZ1		 rs10500264-?
rs8049439-G
rs2412973-?
rs1250550-?		 0.18
0.37
0.46
0.68		 4 x 10-10
2 x 10-9
2 x 10-9
6 x 10-9 		1.21 [1.11-1.31]
1.14 [1.00-1.30]
1.15 [1.01-1.31]
1.16 [1.09-1.25]		 Illumina
[~500,000]		 N
12/10/09 Satake
November 15, 2009
Nat Genet
Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease. 		Parkinson's disease 988 Japanese cases, 2,521 Japanese controls 933 Japanese cases, 15,753 Japanese controls 4q22.1
1q32.1
4p15.32
12q12		 SNCA
PARK16, SLC45A3, NUCKS1, RAB7L1, SLC41A1, PM20D1
BST1
LRRK2		 rs11931074-?
rs947211-?
rs4538475-?
rs1994090-?		 NR
NR
NR
NR		 7 x 10-17
2 x 10-12
3 x 10-9
3 x 10-8 		1.37 [1.27-1.48]
1.3 [1.21-1.39]
1.24 [1.16-1.34]
1.39 [1.24-1.56]		 Illumina
[435,470]		 N
12/10/09 Simon-Sanchez
November 15, 2009
Nat Genet
Genome-wide association study reveals genetic risk underlying Parkinson's disease. 		Parkinson's disease 1,713 European ancestry cases, 3,978 European ancestry controls 3,361 European ancestry cases, 4,573 European ancestry controls 17q21.31
4q22.1
17q21.31
10q24.32
1q32.1
4q22.1
4q21.1
14q22.2
10p13
20p12.1		 MAPT, C17orf69, KIAA1267, LOC644246, IMP5
SNCA
NSF
CYP17A1, C10orf32, CNNM2, SFXN2
PARK16, NUCKS1
MMRN1
STBD1
BMP4
ITGA8
C20orf82		 rs393152-A
rs2736990-C
rs199533-C
rs17115100-G
rs823128-A
rs6532197-G
rs6812193-C
rs12431733-T
rs7077361-T
rs1223271-G		 0.82
0.51
0.83
0.91
0.97
0.09
0.66
0.48
0.89
0.87		 2 x 10-16
2 x 10-16
1 x 10-14
7 x 10-8
7 x 10-8
1 x 10-7
4 x 10-7
3 x 10-6
5 x 10-6
5 x 10-6 		1.3 [NR]
1.23 [NR]
1.28 [NR]
1.25 [NR]
1.52 [NR]
1.32 [NR]
1.12 [NR]
1.13 [NR]
1.19 [NR]
1.18 [NR]		 Illumina
[463,185]		 N
01/07/10 Docherty
November 10, 2009
Genes Brain Behav
A genome-wide association study identifies multiple loci associated with mathematics ability and disability 		Mathematical ability 600 high-performing Caucasian children, 600 low-performing Caucasian children 2,069 Caucasian children NS NS NS NS NS NS Affymetrix
[358,948] (pooled)		 N
12/04/09 Mathias
November 10, 2009
J Allergy Clin Immunol
A genome-wide association study on African-ancestry populations for asthma 		Asthma 464 African American cases, 471 African American controls, 1,028 African Caribbean family members 994 European descent cases, 1,243 European descent controls; 2,331 African descent cases, 2,874 African descent controls (includes family members) NS NS NS NS NS NS Illumina
[~644,503]		 N
12/03/09 Palmer
November 10, 2009
Diabetologia
Candidate loci for insulin sensitivity and disposition index from a genome-wide association analysis of Hispanic participants in the Insulin Resistance Atherosclerosis (IRAS) Family Study 		Insulin traits 229 Hispanic family members 814 Hispanic family members NS NS NS NS NS NS Illumina
[309,200]		 N
12/04/09 Kim
November 06, 2009
J Hum Genet
Identification of 15 loci influencing height in a Korean population. 		Height 8,842 Korean individuals NR 6p21.31
3q23
12q23.2
9p22.3
17q23.2
8q12.1
9q22.32
9q31.3
2p16.1
20q13.32
8q24.11
2p22.3
12q23.2
17q21.2
6p21.1		 HMGA1, C6orf1, NUDT3
ZBTB38, ACPL2
IGF1
FREM1
C17orf82, TBX2, TBX4
PLAG1
FBP2
PALM2-AKAP2
EFEMP1
ANKRD60
EXT1
LTBP1
NUP37, C12orf48, PMCH
KRT23, KRT20
SUPT3H		 rs6918981-G
rs10513137-A
rs1520223-C
rs10961780-G
rs2079795-T
rs13273123-C
rs16910061-T
rs7032940-A
rs3791675-G
rs4811971-C
rs11989122-T
rs41464348-T
rs2292303-C
rs2315504-C
rs10948197-C		 0.21
0.26
0.26
0.33
0.33
0.07
0.14
0.21
0.23
0.39
0.48
0.35
0.30
0.01
0.34		 2 x 10-8
8 x 10-8
9 x 10-7
2 x 10-6
3 x 10-6
3 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6 		.55 [NR] cm increase
.49 [NR] cm increase
.56 [NR] cm decrease
.4 [NR] cm decrease
.4 [NR] cm increase
.75 [NR] cm decrease
.53 [NR] cm decrease
1.32 [NR] cm increase
.45 [NR] cm increase
.7 [NR] cm increase
.36 [NR] cm decrease
.37 [NR] cm decrease
.51 [NR] cm decrease
1.9 [NR] cm increase
.51 [NR] cm decrease		 Affymetrix
[334,546]		 N
12/04/09 Schaefer
November 06, 2009
Hum Mol Genet
A genome-wide association study identifies GLT6D1 as a susceptibility locus for periodontitis. 		Periodontitis 283 German cases, 972 German controls 602 Dutch cases, 577 Dutch controls 9q34.3 GLT6D1 rs1537415-G 0.38 6 x 10-9 1.59 [1.36-1.86] Affymetrix
[345,646]		 N
12/03/09 Birlea
November 05, 2009
J Invest Dermatol
Genome-wide association study of generalized vitiligo in an isolated European founder population identifies SMOC2, in close proximity to IDDM8. 		Vitiligo 32 Romanian cases, 44 Romanian controls NR 6q27
21q22.11
18q21.31
2p16.3		 SMOC2
HUNK
ATP8B1
KCNK12		 rs13208776-?
rs2833607-?
rs10503019-?
rs6544997-?		 0.38
0.26
0.28
0.47		 9 x 10-8
2 x 10-6
3 x 10-6
7 x 10-6 		NR
NR
NR
NR		 Illumina
[297,342]		 N
12/04/09 Medland
November 04, 2009
Am J Hum Genet
Common variants in the trichohyalin gene are associated with straight hair in Europeans. 		Hair morphology 1,649 Australian siblings, 3,196 Australian twins, 16,140 European descent individuals NR 1q21.3
1q21.3
4q21.21
2p21
2q35
2p24.3
20p13
2p21
1q21.3
1q21.3
4q32.2
14q31.1
8p23.2
2p25.1
4q25		 TCHH
AL450992.4
FRAS1
THADA
WNT10A
AC113608.1
AL121890.2
AC016912.4
LCE5A
AL591893.2
NAF1
TSHR
AC019176.2
AC096559.2
EGF		 rs11803731-A
rs10788819-T
rs1268789-T
rs6732426-T
rs7349332-T
rs7586898-C
rs261360-A
rs12623288-A
rs908922-A
rs3124314-T
rs6840361-C
rs8017455-T
rs1454292-T
rs17605562-T
rs17316633-A		 0.82
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-31
2 x 10-8
7 x 10-8
1 x 10-7
1 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
6 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6 		6.11 [NR] % variance
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[~1 million] (imputed)		 N
12/28/09 Craig
November 01, 2009
Diabet Med
Genome-wide SNP genotyping study using pooled DNA to identify candidate markers mediating susceptibility to end-stage renal disease attributed to Type 1 diabetes 		End-stage renal disease 547 Caucasian cases, 549 Caucasian controls NR NS NS NS NS NS NS Illumina
[474,050] (pooled)		 N
12/01/09 Tanaka
October 30, 2009
Blood
A genome-wide association analysis of serum iron concentrations. 		Serum iron concentration 1,919 European descent individuals 569 females 22q12.3 TMPRSS6 rs4820268-A 0.54 5 x 10-9 4.39 [2.90-5.88] ug/dL increase Illumina
[475,322]		 N
12/01/09 Guo
October 29, 2009
J Bone Miner Res
PTH and IL21R May Underlie Variation of Femoral Neck Bone Mineral Density as Revealed by a Genome-Wide Association Study. 		Bone mineral density 983 Caucasian individuals 2,557 Caucasian individuals from 750 families 11p15.2
16p12.1		 PTH
IL21R		 rs9630182-T
rs8057551-G		 0.38
0.32		 4 x 10-7
2 x 10-6 		.11 [NR] s.d. increase
.11 [NR] s.d. increase		 Affymetrix
[342,854]		 N
11/20/09 Paterson
October 29, 2009
Diabetes
A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both HbA1c and glucose 		Glycemic control in type 1 diabetes (HbA1c) 1,304 diabetics 1,382 diabetics, up to 37,436 non-diabetics NS NS NS NS NS NS Affymetrix and Illumina
[2,518,578] (imputed)		 N
11/30/09 Aberg
October 27, 2009
Biol Psychiatry
Genomewide association study of movement-related adverse antipsychotic effects. 		Response to antipsychotic therapy (extrapyramidal side effects) 738 schizophrenic individuals NR 2p12
4q24
11q24.1
14q11.2
9p21.3
8p23.1
14q32.2
16p13.2
2q37.3
9q33.1
1q41
1q41
4q22.1
9q33.2
1p32.1
20q13.32
11p13		 Intergenic
Intergenic
ZNF202
Intergenic
Intergenic
Intergenic
Intergenic
A2BP1
Intergenic
Intergenic
Intergenic
MOSC2
KIAA0914
Intergenic
FGGY
ZNF831
TRIM44		 rs17022444-?
rs7669317-?
rs2126709-?
rs12147450-?
rs10811771-?
rs2251301-?
rs1459148-?
rs9302841-?
rs6743931-?
rs876347-?
rs337161-?
rs1494373-?
rs16996151-?
rs4837752-?
rs17119280-?
rs12625057-?
rs7928794-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-10 (SAS)
8 x 10-8 (AIMS)
4 x 10-7 (SAS)
6 x 10-7 (BARS)
8 x 10-7 (SAS)
1 x 10-6 (BARS)
2 x 10-6 (SAS)
2 x 10-6 (AIMS)
2 x 10-6 (AIMS)
2 x 10-6 (SAS)
3 x 10-6 (SAS)
6 x 10-6 (SAS)
6 x 10-6 (SAS)
6 x 10-6 (SAS)
7 x 10-6 (SAS)
7 x 10-6 (SAS)
8 x 10-6 (SAS)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[492,000]		 N
01/07/10 Sebastiani
October 23, 2009
Am J Hematol
Genetic modifiers of the severity of sickle cell anemia identified through a genome-wide association study 		Sickle cell anemia (severity) 177 African American severe patients, 1,088 African American mild patients 68 severe patients, 95 mild patients NS NS NS NS NS NS Illumina
[~600,000]		 N
11/18/09 Johansson
October 22, 2009
Obesity (Silver Spring)
Linkage and genome-wide association analysis of obesity-related phenotypes: association of weight with the MGAT1 gene. 		Body mass index Up to 3,925 European individuals NR 1p36.33
4q34.3
2q36.1
3q28
19p13.3
19q13.3
3p14.1
5q35.3
9p22.3
11q14.1		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 rs3934834-G
rs2383393-G
rs824931-G
rs1152846-G
rs3803915-C
rs1878047-G
rs1024889-G
rs12517906-G
rs1927702-G
rs1458095-G		 0.80
0.63
0.35
0.77
0.89
0.37
0.28
0.85
0.42
0.90		 6 x 10-7 (females + males)
2 x 10-6 (males)
3 x 10-6 (females + males)
3 x 10-6 (females +males)
5 x 10-6 (females + males)
5 x 10-6 (females + males)
6 x 10-6 (males)
6 x 10-6 (females)
6 x 10-6 (females)
7 x 10-6 (females)		 .11 [NR] kg increase
.1 [NR] kg increase
.07 [NR] kg increase
.09 [NR] kg decrease
.13 [NR] kg decrease
.06 [NR] kg decrease
.12 [NR] kg increase
.16 [NR] kg decrease
.08 [NR] kg increase
.19 [NR] kg increase		 Illumina
[318,237]		 N
11/18/09 " Weight Up to 3,925 European individuals NR 5q35.3
18q11.2
17q24.1
10q22.2
12p11.21
13q12.12
3q28
10q22.1
9p13.3		 MGAT1
NR
NR
NR
NR
NR
NR
NR
NR		 rs12517906-G
rs1840440-G
rs7209395-G
rs7919006-G
rs10844154-C
rs2765086-G
rs1152846-G
rs1816002-G
rs10972341-G		 0.85
0.61
0.23
0.95
0.54
0.94
0.77
0.46
0.60		 7 x 10-8 (females)
3 x 10-7 (females)
3 x 10-6 (females + males)
4 x 10-6 (females)
4 x 10-6 (females)
6 x 10-6 (females)
6 x 10-6 (females + males)
8 x 10-6 (females)
9 x 10-6 (males)		 2.96 [NR] kg decrease
2.16 [NR] kg increase
1.75 [NR] kg increase
4 [NR] kg decrease
1.87 [NR] kg increase
3.86 [NR] kg decrease
1.7 [NR] kg decrease
2.08 [NR] kg increase
2.32 [NR] kg increase		 Illumina
[318,237]		 N
11/25/09 Garriock
October 19, 2009
Biol Psychiatry
A genomewide association study of citalopram response in major depressive disorder. 		Response to citalopram treatment Up to 883 responders, 608 non-responders NR 7q36.3
7q36.3
20q13.31
20q13.31
21q21.3
15q22.2
18q12.1		 UBE3C
UBE3C
BMP7
BMP7
EIF4A1P
RORA
NOL4		 rs6966038-?
rs6966038-?
rs6127921-?
rs6127921-?
rs2830840-?
rs809736-?
rs7239368-?		 0.20
0.19
0.81
0.82
0.46
0.17
0.42		 4 x 10-7 (remission)
5 x 10-7 (response)
1 x 10-6 (remission)
3 x 10-6 (response)
5 x 10-6 (remission)
8 x 10-6 (response)
9 x 10-6 (remission)		 1.68 [1.37-2.04]
1.64 [1.35-1.99]
1.75 [1.39-2.17]
1.64 [1.33-2.04]
1.47 [1.23-1.72]
1.52 [1.27-1.83]
1.45 [1.22-1.69]		 Affymetrix
[430,198]		 N
11/12/09 Kim
October 19, 2009
Neurobiol Dis
Common CYP7A1 Promoter Polymorphism Associated With Risk of Neuromyelitis Optica 		Neuromyelitis optica 53 Korean cases, 240 Korean controls 40 Korean cases NS NS NS NS NS NS Illumina
[288,025]		 N
11/09/09 Han
October 18, 2009
Nat Genet
Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. 		Systemic lupus erythematosus 1,047 Chinese Han cases, 1,205 Chinese Han controls 3,152 Chinese Han cases, 7,050 Chinese Han controls 2q32.3
1q25.1
11q24.3
8p23.1
7p12.2
7q32.1
6q23.3
11q23.3
22q11.21
2p22.3
6p21.32
6q21
10q11.22
12q24.32
5q33.1
7q11.23
16p11.2
16p11.2		 STAT4
TNFSF4
ETS1
BLK
IKZF1
IRF5
TNFAIP3
NR
HIC2, UBE2L3
RASGRP3
HLA-DRB1
PRDM1, ATG5
LRRC18, WDFY4
SLC15A4
TNIP1
NR
NR
NR		 rs7574865-A
rs2205960-A
rs6590330-A
rs7812879-G
rs4917014-A
rs4728142-A
rs2230926-C
rs4639966-G
rs131654-A
rs13385731-A
rs9271100-?
rs548234-G
rs1913517-A
rs1385374-A
rs10036748-A
rs1167796-G
rs7197475-A
rs7186852-A		 0.33
0.27
0.34
0.76
0.68
0.13
0.04
0.30
0.48
0.85
NR
0.26
0.29
0.20
0.76
0.71
0.08
0.08		 5 x 10-42
3 x 10-32
2 x 10-25
2 x 10-24
3 x 10-23
8 x 10-19
1 x 10-17
1 x 10-16
1 x 10-16
1 x 10-15
1 x 10-12
5 x 10-12
7 x 10-12
2 x 10-11
2 x 10-9
2 x 10-8
3 x 10-8
3 x 10-7 		1.51 [1.43-1.61]
1.46 [1.37-1.56]
1.37 [1.29-1.45)
1.45 [1.35-1.56]
1.39 [1.30-1.47]
1.43 [1.32-1.54]
1.72 [1.52-1.94]
1.29 [1.22-1.37]
1.28 [1.20-1.35]
1.43 [1.32-1.56]
1.9 [1.59-2.27]
1.25 [1.17-1.33]
1.24 [1.17-1.32]
1.26 [1.18-1.35]
1.23 [1.15-1.33]
1.2 [1.12-1.28]
1.31 [1.20-1.46]
1.29 [1.17-1.42]		 Illumina
[493,955]		 N
11/09/09 Landi
October 15, 2009
Am J Hum Genet
A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. 		Lung adenocarcinoma 5,739 European descent cases, 5,848 European descent controls 7,561 European descent cases, 13,818 European descent controls 15q25.1
6p21.33
5p15.33
5p15.33
6p22.1		 CHRNA3, CHRNA5
BAT3, APOM
TERT
CLPTM1L
TRNAA-UGC		 rs1051730-T
rs3117582-C
rs2736100-G
rs31489-C
rs4324798-A		 0.35
0.10
0.50
0.59
0.09		 2 x 10-51
5 x 10-12
2 x 10-10
2 x 10-10
2 x 10-8 		1.31 [1.27-1.36]
1.22 [1.15-1.29]
1.12 [1.08-1.16]
1.12 [1.09-1.16]
1.16 [1.09-1.24]		 Illumina
[515,922]		 N
11/05/09 Benyamin
October 11, 2009
Nat Genet
Common variants in TMPRSS6 are associated with iron status and erythrocyte volume. 		Serum markers of iron status 4,818 Australian siblings 3,470 Dutch individuals 22q12.3
6p22.1
22q12.3
6p22.1		 TMPRSS6
HFE
TMPRSS6
HFE		 rs855791-T
rs1800562-A
rs855791-T
rs1800562-A		 0.42
0.08
0.42
0.08		 1 x 10-10 (MCV)
2 x 10-8 (MCV)
5 x 10-7 (Hgb)
5 x 10-7 (Hgb)		 .13 [0.09-0.17] s.d. decrease
.22 [0.14-0.30] s.d. increase
.1 [0.06-0.14] s.d. decrease
.2 [0.12-0.28] s.d. increase		 Illumina & Perlegen
[427,037]		 N
11/05/09 Chambers
October 11, 2009
Nat Genet
Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels. 		Hemoglobin 6,316 Europeans, 9,685 Indian Asians 5,187 Europeans, 6,721 Indian Asians 22q12.3
6p22.1		 TMPRSS6
HFE		 rs855791-A
rs198846-A		 0.53
NR		 2 x 10-13
1 x 10-8 		.13 [0.09-0.17] g/dl decrease
NR		 Affymetrix, Illumina & Perlegen
[NR]		 N
11/03/09 Ganesh
October 11, 2009
Nat Genet
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. 		Hematocrit 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
2p21
7q36.1
10q21.3
22q12.3
12q24.12
7q22.1
6p22.1		 HBS1L, MYB
PRKCE
PRKAG2
HK1
TMPRSS6
SH2B3, ATXN2
TFR2
HFE		 rs9483788-C
rs10168349-C
rs10224002-G
rs16926246-T
rs2413450-T
rs11065987-G
rs7385804-C
rs1800562-A		 NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-15
4 x 10-15
6 x 10-15
1 x 10-13
2 x 10-13
1 x 10-12
4 x 10-10
2 x 10-9 		.22 [0.16-0.28] % increase
.19 [0.14-0.23] % increase
.2 [0.15-0.25] % increase
.33 [0.24-0.42] % increase
.17 [0.13-0.22] % decrease
.17 [0.12-0.22] % decrease
.15 [0.10-0.20] % decrease
.31 [0.21-0.41] % increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Hemoglobin 24,167 European ancestry individuals 9,456 European ancestry individuals 22q12.3
6p22.1
7q36.1
2p21
12q24.12
10q21.3
20q13.2		 TMPRSS6
HFE
PRKAG2
PRKCE
TRAFD1
HK1
TSHZ2		 rs855791-A
rs1800562-A
rs10224002-G
rs10495928-G
rs11065987-A
rs16926246-T
rs6013509-A		 NR
NR
NR
NR
NR
NR
NR		 3 x 10-25
6 x 10-19
3 x 10-15
7 x 10-13
1 x 10-11
2 x 10-11
1 x 10-10 		.09 [0.07-0.11] g/dl decrease
.16 [0.13-0.20] g/dl increase
.07 [0.05-0.09] g/dl increase
.06 [0.05-0.08] g/dl increase
.06 [0.04-0.08] g/dl increase
.11 [0.08-0.14] g/dl increase
.06 [0.05-0.08] g/dl decrease		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Mean corpuscular hemoglobin 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
6p22.2
22q12.3
6p21.1
6q24.1
9p24.1
3q29
19p13.13
16p13.3		 HBS1L, MYB
SLC17A3
TMPRSS6
CCND3, BYSL
CITED2
RCL1
TFRC
GCDH
ITFG3		 rs7776054-G
rs1408272-G
rs2413450-T
rs9349205-A
rs628751-C
rs10758658-A
rs11915082-A
rs11085824-G
rs1122794-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 7 x 10-69
4 x 10-39
9 x 10-34
8 x 10-20
1 x 10-17
2 x 10-14
8 x 10-13
1 x 10-11
3 x 10-10 		.01 [0.009-0.0111] pg decrease
.02 [0.01-0.02] pg decrease
.01 [0.0005-0.007] pg decrease
.01 [0.004-0.006] pg decrease
0 [0.003-0.005] pg decrease
0 [0.004-0.006] pg decrease
0 [0.003-0.005] pg increase
0 [0.003-0.005] pg decrease
0 [0.003-0.006] pg increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Mean corpuscular volume 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
6p22.1
22q12.3
6p21.1
6q24.1
9p24.1
22q13.33
4q12
2p16.1
3q29
7p12.2
16p13.3
19p13.13
7q22.1
10q11.21
6q21
14q23.3		 HBS1L, MYB
HFE
TMPRSS6
CCND3, BYSL
CITED2
RCL1
ECGF1
KIT
BCL11A
TFRC
IKZF1
ITFG3
RTBDN
TFR2
MARCH8
CD164
FNTB		 rs4895441-G
rs1800562-A
rs2413450-T
rs9349205-A
rs643381-A
rs10758658-A
rs131794-A
rs172629-G
rs2540917-C
rs9859260-C
rs12718597-A
rs7189020-T
rs7255045-A
rs7786877-G
rs11239550-G
rs9374080-C
rs4466998-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 7 x 10-86
1 x 10-46
3 x 10-41
1 x 10-31
5 x 10-25
3 x 10-20
1 x 10-15
1 x 10-15
1 x 10-14
8 x 10-14
5 x 10-13
2 x 10-12
2 x 10-12
3 x 10-11
1 x 10-10
4 x 10-10
5 x 10-8 		.01 [0.007-0.009] fl decrease
.01 [0.010-0.014] fl increase
.01 [0.004-0.006] fl decrease
.01 [0.004-0.006] fl decrease
0 [0.003-0.005] fl decrease
0 [0.003-0.005] fl decrease
0 [0.003-0.005] fl decrease
0 [0.003-0.006] fl decrease
0 [0.002-0.004] fl decrease
0 [0.002-0.004] fl increase
0 [0.002-0.004] fl increase
0 [0.002-0.004] fl decrease
0 [0.002-0.004] fl decrease
0 [0.002-0.004] fl increase
0 [0.002-0.003] fl decrease
0 [0.002-0.003] fl decrease
0 [0.001-0.003] fl increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
11/03/09 " Other erythrocyte phenotypes 24,167 European ancestry individuals 9,456 European ancestry individuals 6q23.3
6q23.3
1q23.1
7q22.1		 HBS1L, MYB
HBS1L, MYB
SPTA1
EPO		 rs9483788-G
rs9373124-C
rs857721-A
rs2075671-A		 NR
NR
NR
NR		 1 x 10-47 (RBC)
7 x 10-14 (MCHC)
1 x 10-10 (MCHC)
1 x 10-9 (RBC)		 0 [0.012-0.016] 1 M cells/mm^3 increase
0 [0.002-0.003] g/dl decrease
0 [0.001-0.002] g/dl decrease
0 [0.005-0.009] 1 M cell/mm^3 increase		 Affymetrix & Illumina
[~2.5 million](imputed)		 N
10/30/09 Soranzo
October 11, 2009
Nat Genet
A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. 		Hematological parameters 4,627 European individuals 9,316 European individuals 6q23.3
6p22.1
6p21.1
9p24.1
12q24.13
22q12.3
6p21.31
7q22.1
22q12.3
17q12
6p21.32
6q21		 HBS1L, MYB
HFE
BYSL, CCND3
AK3
PTPN11
FBX07
BAK1
TFR2
TMPRSS6
GSDMA, ORMDL3
Intergenic
Intergenic		 rs9402686-A
rs1800562-A
rs11970772-T
rs385893-C
rs11066301-G
rs9609565-G
rs210135-A
rs7385804-C
rs5756506-C
rs17609240-G
rs2227139-G
rs4947019-G		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 7 x 10-42 (MCV)
1 x 10-23 (MCV)
7 x 10-19 (MCV)
9 x 10-17 (PLT)
8 x 10-12 (PLT)
4 x 10-10 (MCV)
4 x 10-10 (PLT)
5 x 10-10 (RBC)
1 x 10-9 (MCH)
9 x 10-9 (WBC)
1 x 10-7 (WBC)
8 x 10-6 (MCV)		 .82 [0.70-0.94] fl increase
1.41 [1.13-1.69] fl increase
.58 [0.44-0.70] fl increase
6.26 [4.78-7.74] 10^9/l increase
4.65 [3.32-5.98] 10^9/l increase
.37 [0.25-0.49] fl increase
5.44 [3.74-7.14] 10^9/l increase
.01 [0.004-0.008] 10^12/l increase
.14 [0.10-0.18] pg increase
.02 [0.01-0.03] 10^9/l increase
.02 [0.01-0.03] 10^9/l increase
.01 [0.003-0.011] fl decrease		 Affymetrix and Illumina
[~2.11 million] (imputed)		 N
10/30/09 " Mean platelet volume 4,627 European individuals 9,316 European individuals 12q24.31
7q22.3
3p14.3
17q11.2
10q21.3
1q32.1
11p15.5
1q24.3
2p23.1
20p13
18q22.2
15q22.2
5q33.3
20p12.1
12q13.13		 WDR66
PIK3CG
ARHGEF3
TAOK1
JMJD1C
TMCC2
BET1L
DNM3
EHD3
SIRPA
CD226
TPM1
NR
NR
NR		 rs7961894-T
rs342293-G
rs12485738-A
rs2138852-T
rs2393967-A
rs1668873-G
rs11602954-G
rs10914144-C
rs647316-A
rs6136489-T
rs893001-C
rs11071720-T
rs1473247-C
rs6110278-T
rs10506328-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-44
2 x 10-33
6 x 10-31
1 x 10-22
3 x 10-21
1 x 10-20
1 x 10-14
2 x 10-14
3 x 10-11
8 x 10-11
1 x 10-10
2 x 10-8
3 x 10-7
4 x 10-7
5 x 10-7 		.03 [0.027-0.035] fl increase
.02 [0.013-0.017] fl increase
.02 [0.013-0.017] fl increase
.02 [0.012-0.020] fl increase
.01 [0.01-0.018] fl increase
.01 [0.01-0.014] fl increase
.01 [0.009-0.017] fl increase
.01 [0.009-0.017] fl increase
.01 [0.006-0.014] fl increase
.01 [0.006-0.014] fl increase
.01 [0.007-0.015] fl increase
.01 [0.007-0.015] fl increase
.01 [0.004-0.012] fl decrease
.01 [0.005-0.013] fl increase
.01 [0.004-0.012] fl increase		 Affymetrix and Illumina
[~2.11 million] (imputed)		 N
10/23/09 Weiss
October 08, 2009
Nature
A genome-wide linkage and association scan reveals novel loci for autism. 		Autism 1,031 families with 1,553 affected offspring (multiple races/ethnicities) 2,073 trios (multiple races/ethnicities) 5p15.2 SEMA5A, TAS2R1 rs10513025-? NR 3 x 10-7 1.81 [NR] Affymetrix
[~365,000]		 N
10/16/09 Rivadeneira
October 04, 2009
Nat Genet
Twenty bone-mineral-density loci identified by large-scale meta-analysis of genome-wide association studies. 		Bone mineral density (hip) 19,195 European individuals NR 5q14.3
1p31.3
7q21.3
6q25.1
11p15.2
3p22.1
11p11.2
8q24.12
17q21.31
1p36.12
16q24.1
4q22.1
17q21.31		 MEF2C
GPR177
FLJ42280
ESR1
SOX6
CTNNB1
ARHGAP1
TNFRSF11B
HDAC5
ZBTB40
FOXL1
MEPE
CRHR1		 rs1366594-C
rs2566755-C
rs7781370-T
rs2941740-G
rs7117858-G
rs87938-A
rs7932354-T
rs11995824-G
rs228769-G
rs6426749-C
rs10048146-G
rs1471403-T
rs9303521-T		 0.45
0.21
0.34
0.43
0.20
0.45
0.29
0.55
0.20
0.17
0.19
0.34
0.46		 1 x 10-13
2 x 10-12
5 x 10-12
2 x 10-10
6 x 10-10
8 x 10-10
4 x 10-9
7 x 10-9
2 x 10-8
9 x 10-8
2 x 10-7
8 x 10-7
4 x 10-6 		.09 [0.07-0.11] s.d. decrease
.1 [0.07-0.13] s.d. increase
.08 [0.06-0.10] s.d. decrease
.07 [0.05-0.09] s.d. increase
.09 [0.06-0.12] s.d. increase
.07 [0.05-0.09] s.d. decrease
.07 [0.05-0.09] s.d. increase
.07 [0.05-0.09] s.d. decrease
.08 [0.05-0.11] s.d. increase
.08 [0.05-0.11] s.d. increase
.09 [0.06-0.12] s.d. decrease
.06 [0.04-0.08] s.d. increase
.06 [0.04-0.07] s.d. decrease		 Affymetrix & Illumina
[2,543,686](imputed)		 N
10/16/09 " Bone mineral density (spine) 19,195 European individuals NR 13q14.11
8q24.12
1p31.3
6q25.1
7q21.3
1p36.12
7p14.1
11p13
18q21.33
12q13.13
17q21.31
16q24.1
2p16.2
4q22.1
11q13.2
17q21.31		 AKAP11
TNFRSF11B
GPR177
ESR1
FLJ42280
ZBTB40
STARD3NL
DCDC5
TNFRSF11A
SP7
CRHR1
FOXL1
SPTBN1
MEPE
LRP5
HDAC5		 rs9533090-T
rs2062377-T
rs1430742-C
rs2504063-A
rs4729260-G
rs7524102-G
rs1524058-T
rs16921914-A
rs884205-A
rs2016266-G
rs9303521-T
rs10048146-G
rs11898505-A
rs1471403-T
rs599083-G
rs228769-G		 0.50
0.44
0.21
0.40
0.32
0.17
0.40
0.27
0.27
0.32
0.46
0.19
0.34
0.34
0.31
0.20		 5 x 10-25
4 x 10-16
3 x 10-13
6 x 10-11
2 x 10-10
3 x 10-10
1 x 10-9
2 x 10-9
9 x 10-9
1 x 10-8
1 x 10-8
2 x 10-8
2 x 10-8
2 x 10-8
5 x 10-8
4 x 10-6 		.12 [0.10-0.14] s.d. decrease
.09 [0.07-0.11] s.d. increase
.11 [0.07-0.14] s.d. increase
.08 [0.06-0.10] s.d. decrease
.08 [0.05-0.11] s.d. decrease
.09 [0.06-0.12] s.d. increase
.07 [0.05-0.09] s.d. decrease
.08 [0.05-0.11] s.d. increase
.08 [0.05-0.11] s.d. decrease
.07 [0.05-0.09] s.d. increase
.07 [0.05-0.09] s.d. decrease
.09 [0.06-0.12] s.d. decrease
.07 [0.05-0.09] s.d. increase
.07 [0.05-0.09] s.d. increase
.07 [0.05-0.09] s.d. decrease
.07 [0.04-0.10] s.d. increase		 Affymetrix & Illumina
[2,543,686](imputed)		 N
11/04/09 Hicks
October 02, 2009
PLoS Genet
Genetic determinants of circulating sphingolipid concentrations in European populations. 		Sphingolipid concentrations 4,110 European individuals NR 14q23.2
19p13.2
4p12
20p12.1
11q12.3		 SGPP1
LASS4
ATP10D
SPTLC3
FADS3		 rs7157785-A
rs7258249-G
rs10938494-A
rs680379-A
rs1000778-A		 0.19
0.48
0.23
0.34
0.32		 9 x 10-66 (SM 14:0Mol%)
2 x 10-27 (SM 18:1Mol%)
8 x 10-19 (GluCer)
8 x 10-15 (Cer24:0)
7 x 10-13 (SM 16:1)		 0 [0.001-0.002] mol % increase
0 [0.0007-0.001] mol % increase
.06 [0.04-0.07] unit increase
.1 [0.08-0.13] mol % increase
.62 [0.45-0.78] unit decrease		 Illumina
[318,237]		 N
10/06/09 Roeske
September 29, 2009
Mol Psychiatry
First genome-wide association scan on neurophysiological endophenotypes points to trans-regulation effects on SLC2A3 in dyslexic children. 		Speech perception in dyslexia 200 dyslexic German children 186 dyslexic German children 4q32.1
10q26.3		 CTSO, TDO2, PDGFC
NR		 rs4234898-T
rs4751178-G		 NR
NR		 5 x 10-8 (MMNb)
7 x 10-6 (MMNb)		 NR
NR		 Illumina
[297,086]		 N
10/06/09 Nakanishi
September 25, 2009
PLoS Genet
A genome-wide association analysis identified a novel susceptible locus for pathological myopia at 11q24.1. 		Myopia (pathological) 297 Japanese cases, 934 Japanese controls 533 Japanese cases, 977 Japanese controls 11q24.1 BLID, LOC399959 rs577948-G 0.52 2 x 10-7 1.37 [1.21-1.54] Illumina
[411,777]		 N
10/05/09 Latourelle
September 22, 2009
BMC Med Genet
Genomewide association study for onset age in Parkinson disease. 		Parkinson's disease (age of onset) 857 white familial cases, 440 white idiopathic cases 747 Italian idiopathic cases 11p13
15q12
18q12.1
1q23.3
2p14		 QSER1, PRRG4
OCA2
DSG3
ATF6
AAK1		 rs10767971-T
rs17565841-A
rs1941184-C
rs10918270-A
rs7577851-T		 NR
NR
NR
NR
NR		 5 x 10-7
3 x 10-6
4 x 10-6
8 x 10-6
9 x 10-6 		3.24 [NR] years older
2.84 [NR] years younger
2.28 [NR] years younger
2.26 [NR] years younger
6.85 [NR] years younger		 Illumina and Perlegen
[1,861,750] (imputed)		 N
12/29/09 Eeles
September 20, 2009
Nat Genet
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study. 		Prostate cancer 1,854 European ancestry cases, 1,894 European ancestry controls 19,879 cases, 18,761 controls (European, Chinese, Japanese, African American, Latino, and Hawaiian ancestry) 11p15.5
8p21.2
22q13.2
8q24.21
2q31.1
10q11.23
17q12
17q24.3
4q22.3
4q24
11q13.3
4q22.3
Xp11.22
6q25.3
2p21
7q21.3
3p12.1
2p15
7p15.3		 IGF2, IGF2AS, INS, TH
NKX3.1
NR
NR
ITGA6
NR
NR
NR
PDLIM5
TET2
NR
PDLIM5
NR
NR
THADA
JAZF1
NR
EHBP1
NR		 rs7127900-A
rs1512268-A
rs5759167-T
rs4242384-A
rs12621278-A
rs3123078-T
rs7501939-C
rs1859962-T
rs17021918-C
rs7679673-A
rs7130881-G
rs12500426-A
rs1327301-T
rs651164-A
rs1465618-A
rs6465657-T
rs17181170-G
rs6545977-A
rs12155172-A		 0.20
0.45
0.53
NR
0.94
NR
NR
NR
0.65
0.55
NR
0.46
NR
NR
0.23
NR
NR
NR
0.20		 3 x 10-33
3 x 10-30
6 x 10-29
2 x 10-24
9 x 10-23
1 x 10-19
3 x 10-18
2 x 10-16
4 x 10-15
3 x 10-14
8 x 10-13
1 x 10-11
2 x 10-10
2 x 10-9
2 x 10-8
2 x 10-8
3 x 10-8
5 x 10-7
9 x 10-6 		1.22 [1.17-1.27]
1.18 [1.14-1.22]
1.16 [1.14-1.20]
NR
1.33 [1.25-1.43]
NR
NR
NR
1.11 [1.08-1.15]
1.1 [1.06-1.14]
NR
1.08 [1.05-1.12]
NR
NR
1.08 [1.03-1.12]
NR
NR
NR
1.05 [1.00-1.10]		 Illumina
[541,129]		 N
10/05/09 Gudmundsson
September 20, 2009
Nat Genet
Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. 		Prostate cancer Up to 1,968 Icelandic cases, 35,382 Icelandic controls Up to 11,806 European descent cases, 12,387 European descent controls 8q24.21
8q24.21
8q24.21
11q13.2
19q13.2
3q21.3
8q24.21
17q12		 Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic		 rs1447295-A
rs16902094-G
rs16901979-A
rs11228565-A
rs8102476-C
rs10934853-A
rs445114-T
rs4430796-A		 0.11
0.15
0.04
0.20
0.54
0.28
0.64
0.52		 2 x 10-19
6 x 10-15
3 x 10-14
7 x 10-12
2 x 10-11
3 x 10-10
5 x 10-10
8 x 10-6 		1.58 [1.43-1.74]
1.21 [1.15-1.26]
1.8 [1.55-2.09]
1.23 [1.16-1.31]
1.12 [1.08-1.15]
1.12 [1.08-1.16]
1.14 [1.10-1.19]
1.19 [1.10-1.28]		 Illumina
[310,520]		 N
09/30/09 Le Clerc
September 15, 2009
J Infect Dis
Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03). 		AIDS 85 French cases, 2,049 French controls NR 1p13.3
12p12.1
9p23
1q23.3
8q22.3
2q12.1
9p22.3		 Intergenic
SOX5
Intergenic
RXRG
Intergenic
TGFBRAP1
NR		 rs4118325-G
rs1522232-C
rs1360517-A
rs10800098-A
rs3108919-C
rs1020064-G
rs1556032-C		 0.81
0.52
0.06
0.05
0.27
0.77
0.49		 6 x 10-7
2 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
7 x 10-6
9 x 10-6 		4.17 [2.17-8.33]
2.22 [1.59-3.13]
3.09 [2.00-4.78]
3.29 [2.08-5.20]
2.13 [1.56-2.91]
2.94 [1.75-5.00]
2.05 [1.48-2.84]		 Illumina
[291,119]		 N
09/30/09 Suppiah
September 13, 2009
Nat Genet
IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. 		Response to hepatitis C treatment 131 European ancestry responders, 162 European ancestry non-responders 261 European responders, 294 European non-responders 19q13.2 IL28A, IL28B rs8099917-G NR 9 x 10-9 1.98 [1.57-2.52] Illumina
[311,159]		 N
09/30/09 Tanaka
September 13, 2009
Nat Genet
Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. 		Response to hepatitis C treatment 72 Japanese responders, 82 Japanese non-responders 122 Japanese responders, 50 Japanese non-responders 19q13.2 IL28B rs8099917-G 0.12 3 x 10-32 27.1 [14.6-50.3] Affymetrix
[621,220]		 N
09/30/09 Heinzen
September 11, 2009
J Alzheimers Dis
Genome-Wide Scan of Copy Number Variation in Late-Onset Alzheimer's Disease. 		Alzheimer's disease 331 cases, 368 controls NR 19q13.32
13q13.2
1p31.1
10q24.31
6q24.3		 TOMM40, APOE
RFC3
TTLL7
PAX2
SASH1		 rs2075650-?
rs690705-?
rs7539409-?
rs4509693-?
rs9390537-?		 0.15
0.25
0.18
0.18
0.22		 3 x 10-11
6 x 10-7
1 x 10-6
6 x 10-6
8 x 10-6 		NR
NR
NR
NR
NR		 Illumina
[~550,000]		 N
09/30/09 Sha
September 09, 2009
BMC Med Genet
Genome-wide association reveals three SNPs associated with sporadic amyotrophic lateral sclerosis through a two-locus analysis 		Amyotrophic lateral sclerosis (interaction) 276 Caucasian cases, 271 Caucasian controls NR NS NS NS NS NS NS Illumina
[549,062]		 N
09/29/09 Harold
September 06, 2009
Nat Genet
Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. 		Alzheimer's disease 3,941 European ancestry cases, 7,848 European ancestry controls 2,023 European ancestry cases, 2,340 European ancestry controls 19q13.32
8p21.1
11q14.2		 APOE, TOMM40
CLU
PICALM		 rs2075650-?
rs11136000-?
rs3851179-?		 0.15
0.60
0.63		 2 x 10-157
9 x 10-10
1 x 10-9 		2.53 [2.37-2.71]
1.16 [1.11-1.22]
1.16 [1.11-1.22]		 Illumina
[529,205]		 N
09/29/09 Lambert
September 06, 2009
Nat Genet
Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. 		Alzheimer's disease 2,032 French cases, 5,328 French controls 3,978 European cases, 3,297 European controls 19q13.32
1q32.2
8p21.1		 APOE
CR1
CLU		 rs2075650-?
2-SNP haplotype
3-SNP haplotype		 0.90
0.18
0.26		 2 x 10-16
3 x 10-10 (AA)
6 x 10-10 (CCG)		 NR
1.22 [1.15-1.30]
1.22 [1.14-1.29]		 Illumina
[537,029]		 N
09/29/09 Rung
September 06, 2009
Nat Genet
Genetic variant near IRS1 is associated with type 2 diabetes, insulin resistance and hyperinsulinemia. 		Type 2 diabetes and other traits 679 French cases, 697 French controls 5,579 European cases, 7,096 European controls 10q25.2
6p22.3
2q36.3
4p16.1
8q24.11
5q14.3		 TCF7L2
CDKAL1
LOC64673, IRS1
WFS1, PPP2R2C
SLC30A8
LOC72901, CETN3		 rs7903146-T
rs4712523-G
rs2943641-C
rs4689388-T
rs13266634-C
rs12518099-C		 0.27
0.32
0.63
0.57
0.68
0.23		 1 x 10-30
2 x 10-12
9 x 10-12
1 x 10-8
8 x 10-8
7 x 10-7 		1.48 [1.39-1.57]
1.2 [1.14-1.26]
1.19 [1.13-1.25]
1.16 [1.10-1.21]
1.16 [1.10-1.22]
1.16 [1.10-1.22]		 Illumina
[392,365]		 N
09/29/09 van Es
September 06, 2009
Nat Genet
Genome-wide association study identifies 19p13.3 (UNC13A) and 9p21.2 as susceptibility loci for sporadic amyotrophic lateral sclerosis. 		Amyotrophic lateral sclerosis 2,323 European descent cases, 9,013 European descent controls 2,532 European descent cases, 5,940 European descent controls 19p13.11
9p21.2
9p21.2
Xq13.3
12p12.3
11q22.1
9p21.2
Xp22.32		 UNC13A
MOBKL2B, IFNK, C9orf72
MOBKL2B, IFNK, C9orf72
NR
NR
NR
NR
NR		 rs12608932-?
rs2814707-?
rs3849942-?
rs5937496-?
rs9971637-?
rs2405657-?
rs774359-?
rs5916687-?		 0.34
0.23
0.23
0.13
0.05
0.66
0.25
0.27		 3 x 10-14
7 x 10-9
1 x 10-8
6 x 10-7
2 x 10-6
3 x 10-6
3 x 10-6
3 x 10-6 		1.25 [NR]
1.22 [NR]
1.23 [NR]
1.38 [NR]
1.48 [NR]
1.19 [NR]
1.19 [NR]
1.22 [NR]		 Illumina
[292,768]		 N
10/02/09 Need
September 04, 2009
Hum Mol Genet
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB. 		Cognitive performance 1,295 individuals NR 15q23
Xp22.2
3p22.3
13q34
16p12.1
17q21.32
8q24.13
21q11.2
17q25.2
14q23.2
15q21.3
2q31.1
5p15.31
11q14.2
12p13.1
15q12
1q23.2
20p12.3
21q21.3
3q27.2
16q23.3
3p25.1
7q31.1
18q22.1
1q41
3p22.1
3q26.32
9p22.2
11p12
13q12.3
14q23.2
1p32.1
1q32.1
7p15.1
12q24.23
19q12
1p36.13
3q13.33
4q28.1
7p14.1
7q31.1
8q12.1
11q13.5
6p21.2
18q12.3
Xp22.31
13q14.11		 CORO2B
HCCS
ARPP-21
Intergenic
Intergenic
Intergenic
FAM91A1
NRIP1
SEC14L1
MTHFD1
UNC13C
GORASP2
Intergenic
C11orf73
GRIN2B
GABRB3
VANGL2
PLCB1
JAM2
EHHADH
Intergenic
GRIP2
IMMP2L
C18orf4, DSEL
FAM177B
MOBP
Intergenic
SH3GL2
API5
FLT1
MTHFD1
JUN
MDM4
CPVL
CCDC64
TSHZ3
FAM131C
FBXO40
FAT4
VPS41
IMMP2L
TOX
CAPN5
C6orf129
RIT2
VCX3B
DNAJC15		 rs11856323-?
rs5934953-?
rs6799705-?
rs767210-?
rs2203512-?
rs2326017-?
rs10481151-?
rs2229741-?
rs3744064-?
rs10498514-?
rs1897031-?
rs4668356-?
rs7729273-?
rs6592284-?
rs2160519-?
rs8043440-?
rs16832015-?
rs6056209-?
rs17001239-?
rs7374394-?
rs4082514-?
rs9036-?
rs10279573-?
rs2124349-?
rs6683071-?
rs816488-?
rs7612209-?
rs10810865-?
rs10501293-?
rs17086609-?
rs2295639-?
rs4601609-?
rs12143943-?
rs2252521-?
rs11064994-?
rs1078373-?
rs9442235-?
rs3772130-?
rs12639834-?
rs11984145-?
rs12531640-?
rs960089-?
rs3781684-?
rs904251-?
rs8085804-?
rs7892812-?
rs1324015-?		 0.08
0.02
0.05
0.11
0.14
0.30
0.14
0.47
0.03
0.02
0.18
0.06
0.20
0.21
0.06
0.17
0.01
0.43
0.12
0.20
0.03
0.19
0.14
0.05
0.20
0.04
0.40
0.13
0.25
0.35
0.02
0.05
0.41
0.34
0.06
0.37
0.42
0.23
0.36
0.05
0.13
0.07
0.11
0.38
0.37
0.47
0.42		 1 x 10-7 (PAL8)
1 x 10-7 (PAL6)
2 x 10-7 (PAL8)
3 x 10-7 (PAL6)
3 x 10-7 (PRM)
3 x 10-7 (SWM strategy)
4 x 10-7 (PRM)
6 x 10-7 (SRM)
7 x 10-7 (PAL6)
8 x 10-7 (SWM strategy)
1 x 10-6 (PRM)
1 x 10-6 (PAL8)
1 x 10-6 (SSP)
2 x 10-6 (IED)
2 x 10-6 (IED)
2 x 10-6 (SRM)
2 x 10-6 (IED)
2 x 10-6 (RVP)
2 x 10-6 (PRM)
2 x 10-6 (IED)
3 x 10-6 (PC1)
3 x 10-6 (PAL6)
3 x 10-6 (IED)
4 x 10-6 (IED)
4 x 10-6 (PC1)
4 x 10-6 (IED)
4 x 10-6 (IED)
4 x 10-6 (PAL6)
5 x 10-6 (SWM Strategy)
5 x 10-6 (IED)
5 x 10-6 (SWM Strategy)
5 x 10-6 (PRM)
5 x 10-6 (PAL8)
5 x 10-6 (PAL8)
6 x 10-6 (PAL6)
6 x 10-6 (SSP)
6 x 10-6 (PC1)
6 x 10-6 (PC1)
6 x 10-6 (SWM Strategy)
6 x 10-6 (PAL8)
6 x 10-6 (IED)
6 x 10-6 (PAL6)
7 x 10-6 (VRM)
7 x 10-6 (SWM Strategy)
8 x 10-6 (VRM)
8 x 10-6 (SSP)
9 x 10-6 (PC1)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[475,971]		 N
09/28/09 Paterson
September 03, 2009
Arterioscler Thromb Vasc Biol
Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin. 		Serum soluble E-selectin 685 individuals with type 1 diabetes 477 nondiabetic siblings 9q34.2 ABO rs579459-C 0.20 1 x 10-29 NR Illumina
[~841,000]		 N
09/28/09 Tonjes
September 03, 2009
Hum Mol Genet
Genetic variation in GPR133 is associated with height: genome wide association study in the self-contained population of Sorbs. 		Height 929 Sorbian individuals, 2,986 Caucasian individuals 2,772 German individuals 12q24.33 GPR133 rs1569019-? NR 5 x 10-8 .95 [0.61-1.29] cm increase Affymetrix
[390,619]		 N
09/28/09 De Moor
September 02, 2009
Med Sci Sports Exerc
Genome-Wide Association Study of Exercise Behavior in Dutch and American Adults. 		Exercise (leisure time) 1,644 Dutch individuals, 978 European individuals NR 10q23.2
18p11.32
2q33.1		 PAPSS2
C18orf2
DNAPTP6		 rs10887741-T
rs8097348-G
rs12612420-A		 NR
NR
NR		 4 x 10-6
7 x 10-6
8 x 10-6 		1.32 [1.17-1.49]
1.36 [1.19-1.56]
1.43 [1.22-1.67]		 Affymetrix and Perlegen
[~1.6 million] (imputed)		 N
09/29/09 Ising
September 01, 2009
Arch Gen Psychiatry
A genomewide association study points to multiple loci that predict antidepressant drug treatment outcome in depression 		Response to antidepressant treatment 339 German individuals 1,193 German individuals NS NS NS NS NS NS Illumina
[389,251] (pooled)		 N
09/28/09 McClay
September 01, 2009
Mol Psychiatry
Genome-wide pharmacogenomic analysis of response to treatment with antipsychotics. 		Response to antipsychotic treatment 738 cases NR 4p15.1
9q33.3
12q23.1
2q14.3
1q21.3
6p24.1
15q13.3
3q28
6p21.33		 Intergenic
Intergenic
ANKS1B
CNTNAP5
Intergenic
Intergenic
TRPM1
Intergenic
Intergenic		 rs17390445-?
rs888219-?
rs7968606-?
rs17727261-?
rs10888501-?
rs1040994-?
rs17815774-?
rs7635839-?
rs12526186-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-7 (ziprasidone)
2 x 10-7 (risperidone)
3 x 10-7 (olanzapine)
5 x 10-7 (risperidone)
1 x 10-6 (olanzapine)
2 x 10-6 (olanzapine)
3 x 10-6 (risperidone)
3 x 10-6 (olanzapine)
3 x 10-6 (risperidone)		 17 [NR] % of variance explained
11 [NR] % of variance explained
10 [NR] % of variance explained
10 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained
9 [NR] % of variance explained		 Affymetrix & Perlegen
[492,900]		 N
09/10/09 Spain
September 01, 2009
Cancer Res
Colorectal Cancer Risk Is Not Associated with Increased Levels of Homozygosity in a Population from the United Kingdom 		Colorectal cancer 921 white cases, 929 white controls 1,214 white cases, 1,435 white controls NS NS NS NS NS NS Illumina
[486,303]		 N
09/09/09 Laje
August 31, 2009
Pharmacogenet Genomics
Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients 		Response to antidepressant treatment 90 white cases, 90 white controls 30 white cases, 1,652 white controls NS NS NS NS NS NS Illumina
[100,864]		 N
09/09/09 Hancock
August 28, 2009
PLoS Genet
Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in mexican children. 		Asthma (childhood onset) 492 Mexican trios 177 Mexican trios 9q21.31 TLE4, CHCHD9 rs2378383-? 0.78 7 x 10-7 1.64 [1.32-2.04] Illumina
[520,767]		 N
09/24/09 Liu
August 28, 2009
PLoS One
Powerful bivariate genome-wide association analyses suggest the SOX6 gene influencing both obesity and osteoporosis phenotypes in males. 		Obesity and osteoporosis 499 Caucasian males, 501 Caucasian females 1,370 Caucasian males, 1,985 Caucasian females 11p15.1
11p15.1		 SOX6
SOX6		 rs297325-C
rs4756846-C		 0.23
0.12		 4 x 10-7 (BMI-BMD, males)
5 x 10-7 (BMI-BMD, males)		 NR
NR		 Affymetrix
[379,319]		 N
09/09/09 Shuldiner
August 26, 2009
JAMA
Association of cytochrome P450 2C19 genotype with the antiplatelet effect and clinical efficacy of clopidogrel therapy. 		Response to clopidogrel therapy 429 Amish individuals 140 white, 83 African American, and 4 unspecified individuals 10q23.33 CYP2C18, CYP2C19, CYP2C9, CYP2C8 rs12777823-? 0.17 2 x 10-13 (Amish) NR Affymetrix
[400,230]		 N
09/09/09 Cui
August 18, 2009
Gastroenterology
Functional variants in ADH1B and ALDH2 coupled with alcohol and smoking synergistically enhance esophageal cancer risk. 		Esophageal cancer 188 Japanese cases, 938 Japanese controls 699 Japanese cases, 1,482 Japanese controls 12q24.12
4q23		 BRAP, ALDH2
ADH6, ADH1B		 rs671-A
rs1229984-G		 NR
NR		 3 x 10-24
8 x 10-24 		1.67 [1.58-1.76]
1.79 [1.69-1.88]		 Illumina
[359,195]		 N
09/09/09 Ge
August 16, 2009
Nature
Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. 		Response to hepatitis C treatment 871 Caucasian, 191 African American, and 75 Hispanic participants NR 19q13.2
6q21
4q34.3		 IL28B
AKD2
Intergenic		 rs12979860-C
rs9400317-?
rs17067123-?		 0.72
NR
NR		 1 x 10-28 (combined)
7 x 10-6 (combined)
8 x 10-6 (combined)		 2 [1.8-2.3] (European-Americans)
NR
NR		 Illumina
[565,759]		 N
09/04/09 Papaemmanuil
August 16, 2009
Nat Genet
Loci on 7p12.2, 10q21.2 and 14q11.2 are associated with risk of childhood acute lymphoblastic leukemia. 		Acute lymphoblastic leukemia (childhood) 503 European pediatric cases, 1,438 European pediatric controls 404 European pediatric cases, 960 European pediatric controls 7p12.2
10q21.2
14q11.2		 IKZF1
ARID5B
CEBPE		 rs4132601-C
rs7089424-C
rs2239633-G		 0.28
0.34
0.52		 1 x 10-19
7 x 10-19
3 x 10-7 		1.69 [1.58-1.81]
1.65 [1.54-1.76]
1.34 [1.22-1.45]		 Illumina
[291,473]		 N
09/11/09 Trevino
August 16, 2009
Nat Genet
Germline genomic variants associated with childhood acute lymphoblastic leukemia. 		Acute lymphoblastic leukemia (childhood) 317 European descent cases, 17,958 European descent controls NR 10q21.2
7p12.2
12q24.22
6q24.1
19q13.31
1q43
2q36.1
1p31.1
3q26.32
1q31.3
1q44
10p11.21
12p13.32
18p11.32		 ARID5B
IKZF1, DDC
KRTHB5
Intergenic
ZNF230
RYR2
KCNE4
SIAT7C
KCNMB2
Intergenic
OR2C3
PARD3
C12orf5
Intergenic		 rs10821936-C
rs11978267-G
rs2089222-A
rs11155133-G
rs2191566-G
rs7554607-A
rs12621643-T
rs10873876-T
rs9290663-T
rs6428370-G
rs1881797-C
rs563507-A
rs10849033-G
rs1879352-C		 0.34
0.27
0.03
0.01
0.28
0.56
0.28
0.15
0.13
0.32
0.18
0.04
0.02
0.16		 1 x 10-15
8 x 10-11
8 x 10-8
3 x 10-7
4 x 10-7
2 x 10-6
3 x 10-6
4 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6 		1.91 [1.60-2.20]
1.69 [1.40-1.90]
2.26 [1.60-3.0]
3.62 [2.10-6.00]
1.52 [1.20-1.70]
1.49 [1.20-1.70]
1.48 [1.20-1.70]
1.55 [1.20-1.80]
1.58 [1.20-1.90]
1.43 [1.20-1.60]
1.52 [1.20-1.80]
2 [1.40-2.70]
2.55 [1.60-3.80]
1.53 [1.20-1.80]		 Affymetrix
[307,944]		 N
09/04/09 Alkelai
August 13, 2009
Psychopharmacology (Berl)
Genome-wide association study of antipsychotic-induced parkinsonism severity among schizophrenia patients. 		Response to antipsychotic treatment 199 cases, 198 controls NR 2q24.3 FIGN rs12476047-C NR 3 x 10-6 3.21 [1.97-5.25] Affymetrix & Perlegen
[495,172]		 N
09/09/09 Potkin
August 07, 2009
PLoS One
Hippocampal atrophy as a quantitative trait in a genome-wide association study identifying novel susceptibility genes for Alzheimer's disease. 		Hippocampal atrophy 172 cases, 209 controls NR 21q21.1
5q21.3
9q21.13
14q22.1
13q31.1
20q11.23
20q13.31
5q14.1
7p12.2
7q21.11
9q21.31
12q14.3
1q21.3
20q11.23
5q14.1
12q13.11
5p14.1
5p15.1
7p21.3
11q24.3
8q24.12		 FDPSP
EFNA5
PRUNE2
FRMD6
Intergenic
C20orf132
ZBP1
SCAMP1, LHFPL2
IKZF1
MAGI2
RP11
CAND1
S100A5
RPN2
ARSB
ARID2, SFRS2IP
Intergenic
NR
Intergenic
Intergenic
MAL2		 rs1888414-?
rs10074258-?
rs10781380-?
rs11626056-?
rs4773460-?
rs8115854-?
rs2073145-?
rs6881634-?
rs10276619-?
rs11525066-?
rs10867752-?
rs1082714-?
rs4845552-?
rs6031882-?
rs337847-?
rs1373549-?
rs7727656-?
rs682748-?
rs9918508-?
rs6590322-?
rs1364705-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7
2 x 10-7
7 x 10-7
1 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
3 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[516,645]		 N
09/04/09 Tse
August 05, 2009
Am J Hum Genet
Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3. 		Nasopharyngeal carcinoma 277 Han Chinese cases, 285 Han Chinese controls 635 Han Chinese cases, 1,640 Han Chinese controls 6p21.33
6p22.1
6p22.1		 HLA-A
GABBR1
HLA-F		 rs2517713-A
rs29232-A
rs3129055-G		 0.62
0.46
0.31		 4 x 10-20
9 x 10-17
7 x 10-11 		1.88 [1.65-2.15]
1.67 [1.48-1.88]
1.51 [1.34-1.71]		 Illumina
[480,365]		 N
09/14/09 Broderick
August 04, 2009
Cancer Res
Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study. 		Lung cancer 1,952 European cases, 1,438 European controls 5,608 European cases, 6,767 European controls 15q25.1
6p21.33
5p15.33
10q23.31
15q15.2
3p24.1
2p14		 CHRNA3
BAT3
CLPTM1L
NR
TGM5
NR
NR		 rs8034191-?
rs3117582-?
rs4975616-?
rs1926203-?
rs748404-?
rs1530057-?
rs4254535-?		 NR
NR
NR
NR
NR
NR
NR		 3 x 10-26
4 x 10-10
3 x 10-9
1 x 10-6
1 x 10-6
3 x 10-6
5 x 10-6 		1.29 [1.23-1.35]
1.24 [1.16-1.33]
1.15 [1.10-1.20]
1.12 [NR]
1.15 [1.09-1.20]
1.26 [NR]
1.12 [NR]		 Illumina
[511,919]		 N
09/04/09 Chambers
August 03, 2009
Diabetes
Common genetic variation near melatonin receptor MTNR1B contributes to raised plasma glucose and increased risk of type 2 diabetes among Indian Asians and European Caucasians. 		Fasting plasma glucose 7,474 Indian Asian individuals 4,462 European controls 11q21 MTNR1B rs2166706-G 0.46 2 x 10-9 .07 (0.04-0.09) mmol/L increase Illumina
[up to 544,390]		 N
09/04/09 Grant
August 03, 2009
J Pediatr
A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24. 		Nonsyndromic cleft lip with or without cleft palate 111 European ancestry cases, 5,951 European ancestry controls NR 18q22.3
8q24.21		 Intergenic
Intergenic		 rs17085106-?
rs987525-?		 0.018
0.22		 4 x 10-8
9 x 10-8 		4.07 [2.37-7.00]
2.09 [1.59-2.76]		 Illumina
[495,858]		 N
09/04/09 Amundadottir
August 02, 2009
Nat Genet
Genome-wide association study identifies variants in the ABO locus associated with susceptibility to pancreatic cancer. 		Pancreatic cancer 1,771 European ancestry cases, 1,805 European ancestry controls 2,120 European ancestry cases, 2,127 European ancestry controls 9q34.2 ABO rs505922-C 0.35 5 x 10-8 1.2 [1.12-1.28] Illumina
[558,542]		 N
09/04/09 Song
August 02, 2009
Nat Genet
A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2. 		Ovarian cancer 1,817 European ancestry cases, 2,353 European ancestry controls 6,944 European ancestry cases, 9,477 European ancestry controls 9p22.2 BNC2, LOC648570, CNTLN rs3814113-T 0.68 5 x 10-19 1.22 [1.16-1.27] Illumina
[up to ~2,000,000] (imputed)		 N
08/21/09 Wu
August 02, 2009
Nat Genet
Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer. 		Bladder cancer 969 Caucasian cases, 957 Caucasian controls 5,698 US and European cases, 38,633 US and European controls 8q24.3 PSCA rs2294008-T 0.46 2 x 10-10 1.15 [1.10-1.20] Illumina
[556,429]		 N
12/29/09 Cheng
August 01, 2009
Circ Cardiovasc Genet
Genome-wide association scan identifies variants near Matrix Metalloproteinase (MMP) genes on chromosome 11q21-22 strongly associated with serum MMP-1 levels. 		Serum matrix metalloproteinase 778 Old Order Amish individuals NR 11q22.2
11q22.2
11q22.3
20p11.23		 MMP
MMP-1
MMP-1, MMP-3
SLC24A3		 rs495366-A
rs11225434-C
rs11226373-G
rs3790268-?		 0.36
0.38
0.15
NR		 6 x 10-34
9 x 10-29
2 x 10-18
3 x 10-7 		.44 [NR] unit decrease in ln(MMP-1)
.39 [NR] unit increase in ln(MMP-1)
.44 [NR] unit increase in ln(MMP-1)
NR		 Affymetrix
[338,079]		 N
09/04/09 Comabella
August 01, 2009
Arch Neurol
Genome-wide scan of 500,000 single-nucleotide polymorphisms among responders and nonresponders to interferon beta therapy in multiple sclerosis 		Response to interferon beta therapy 53 responders, 53 non-responders 49 responders, 45 non-responders NS NS NS NS NS NS Affymetrix
[428,867](pooled)		 N
12/29/09 Marroni
August 01, 2009
Circ Cardiovasc Genet
A genome-wide association scan of RR and QT interval duration in 3 European genetically isolated populations: the EUROSPAN project. 		QT interval 2,325 European individuals NR 1q23.3
13q14.2
14q32.13
3q29
4q31.23
3p14.2
4q26
12p12.2
3q21.1
5p15.32
2q24.1
2q31.2
4p15.1
7p14.2		 NOS1AP
Intergenic
TCL6
LOC100132805
ARHGAP10
PTPRG
Intergenic
PDE3A
Intergenic
Intergenic
Intergenic
TTN
Intergenic
ELMO1		 rs2880058-G
rs2478333-A
rs8015016-G
rs789852-A
rs6845865-G
rs652889-A
rs4318720-A
rs1348582-G
rs2650951-A
rs7728043-G
rs7601713-A
rs12476289-A
rs1533317-A
rs10488031-A		 0.32
0.33
0.20
0.08
0.21
0.36
0.09
0.18
0.05
0.48
0.23
0.07
0.46
0.07		 2 x 10-10
4 x 10-8
5 x 10-7
7 x 10-7
7 x 10-7
8 x 10-7
8 x 10-7
1 x 10-6
1 x 10-6
1 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6 		.19 [0.13-0.25] unit increase
.17 [0.11-0.23] unit increase
.18 [0.10-0.26] unit decrease
.25 [0.15-0.35] unit increase
.19 [0.11-0.27] unit increase
.15 [0.09-0.21] unit decrease
.28 [0.16-0.40] unit increase
.2 [0.12-0.28] unit increase
.29 [0.17-0.41] unit decrease
.14 [0.08-0.20] unit decrease
.16 [0.10-0.22] unit decrease
.29 [0.17-0.41] unit increase
.14 [0.08-0.20] unit increase
.26 [0.16-0.36] unit decrease		 Illumina
[~318,327]		 N
12/29/09 " RR interval (heart rate) 2,325 European individuals NR 12q24.33
4q28.3
9q21.31
10p13
13q12.11
18q23
5q12.3
6p21.32
11p12
15q25.1
1q44
2p22.2
3q12.1
9p21.3
1q32.3
2p11.2
2p13.3
8q12.1
9p21.3
22q12.1		 GPR133
Intergenic
Intergenic
FRMD4A
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
RASGRF1
AKT3
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic		 rs885389-A
rs1024020-A
rs12554086-A
rs1541010-A
rs7318731-A
rs2717128-G
rs10514995-G
rs3117035-A
rs1484948-G
rs3743200-A
rs4132509-A
rs4352210-A
rs2670321-C
rs12552736-G
rs17706439-A
rs1447537-A
rs10496166-A
rs3110127-A
rs13300284-A
rs744016-A		 0.30
0.21
0.39
0.28
0.48
0.14
0.36
0.48
0.32
0.27
0.21
0.37
0.27
0.06
0.17
0.31
0.13
0.33
0.04
0.20		 4 x 10-8
4 x 10-7
4 x 10-7
1 x 10-6
1 x 10-6
1 x 10-6
1 x 10-6
1 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6 		.17 [0.11-0.23] unit decrease
.18 [0.10-0.26] unit increase
.16 [0.10-0.22] unit decrease
.15 [0.09-0.21] unit increase
.14 [0.08-0.20] unit decrease
.19 [0.11-0.27] unit decrease
.15 [0.09-0.21] unit increase
.14 [0.08-0.20] unit decrease
.16 [0.10-0.22] unit increase
.16 [0.10-0.22] unit increase
.18 [0.10-0.26] unit decrease
.14 [0.08-0.20] unit decrease
.16 [0.10-0.22] unit decrease
.25 [0.15-0.35] unit increase
.18 [0.10-0.26] unit increase
.15 [0.09-0.21] unit decrease
.18 [0.10-0.26] unit increase
.15 [0.09-0.21] unit decrease
.26 [0.14-0.38] unit increase
.17 [0.09-0.25] unit decrease		 Illumina
[~318,327]		 N
08/21/09 Nakano
July 22, 2009
Proc Natl Acad Sci U S A
Three susceptible loci associated with primary open-angle glaucoma identified by genome-wide association study in a Japanese population 		Glaucoma (primary open-angle) 418 Japanese cases, 300 Japanese controls 409 Japanese cases, 448 Japanese controls NS NS NS NS NS NS Affymetrix
[331,838]		 N
08/21/09 Skibola
July 20, 2009
Nat Genet
Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma. 		Follicular lymphoma 189 European ancestry cases, 592 European controls 456 European ancestry cases, 2,785 European ancestry controls 6p21.33 STG, PSORS1 rs6457327-C 0.62 5 x 10-11 1.69 [1.43-2.00] Illumina
[~500,000] (pooled)		 N
08/12/09 Adeyemo
July 17, 2009
PLoS Genet
A genome-wide association study of hypertension and blood pressure in African Americans. 		Hypertension 509 African American cases, 508 African American controls 366 West African cases, 614 West African controls 15q22.1
4q23		 ALDH1A2
ADH7		 rs1550576-?
rs991316-T		 0.86
0.45		 3 x 10-6
5 x 10-6 		1.92 [NR]
1.62 [NR]		 Affymetrix
[808,465]		 N
08/04/09 Benjamin
July 13, 2009
Nat Genet
Variants in ZFHX3 are associated with atrial fibrillation in individuals of European ancestry. 		Atrial fibrillation 3,413 cases, 37,105 referents 2,145 cases, 4,073 controls 4q25
16q22.3
1p36.22		 PITX2
ZFHX3
MTHFR, NPPA		 rs17042171-A
rs2106261-T
rs17375901-T		 0.12
0.174
0.053		 4 x 10-63
2 x 10-15
6 x 10-7 		1.65
1.25
1.26 		Affymetrix & Illumina
[~2.5 million] (imputed)		 N
07/30/09 Gudbjartsson
July 13, 2009
Nat Genet
A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke. 		Atrial fibrillation 2,385 European cases, 33,752 European controls up to 2,427 European cases, 3,379 European controls 4q25
16q22.3		 Intergenic
ZFHX3		 rs2200733-?
rs7193343-T		 0.12
NR		 1 x 10-14
1 x 10-10 		1.42 [NR]
1.21 [1.14-1.29]		 Illumina
[303,136]		 N
07/24/09 Nolte
July 09, 2009
PLoS One
Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies. 		QT interval 3,558 Caucasian individuals 29,527 Caucasian individuals 1q23.3
6q22.31		 OLFML2B, NOS1AP
SLC35F1, C6orf204, PLN		 rs12143842-T
rs11153730-C		 0.25
0.50		 1 x 10-83
2 x 10-29 		.18 [NR] unit increase
.09 [NR] unit increase		 Affymetrix & Illumina
[~2,399,142] (imputed)		 N
07/24/09 Tonjes
July 08, 2009
Eur J Hum Genet
Association of FTO variants with BMI and fat mass in the self-contained population of Sorbs in Germany 		Body mass index and fat mass 948 Sorbian individuals NR NS NS NS NS NS NS Affymetrix
[390,619]		 N
08/07/09 Vasan
July 08, 2009
JAMA
Genetic variants associated with cardiac structure and function: a meta-analysis and replication of genome-wide association data. 		Aortic root size 12,612 European ancestry individuals 4,094 European ancestry individuals 5q23.2
17p13.3
12q14.3
12p12.2
1p21.2
15q24.1		 CCDC100, PPIC
SMG6, SRR, TSR1, SGSM2
HMGA2
PDE3A
PALMD
LOXL1		 rs17470137-A
rs10852932-T
rs4026608-C
rs10770612-G
rs7543130-A
rs893817-G		 0.29
0.36
0.38
0.19
0.49
0.34		 1 x 10-11
2 x 10-11
2 x 10-9
2 x 10-8
1 x 10-7
3 x 10-6 		.03 [0.02-0.04] cm increase
.03 [0.02-0.04] cm increase
.03 [0.02-0.04] cm decrease
.03 [0.02-0.04] cm increase
.03 [0.02-0.04] cm increase
.02 [0.01-0.03] cm increase		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
08/07/09 " Cardiac structure and function 12,612 European ancestry individuals 4,094 European ancestry individuals 6q22.31
10q23.1
5q22.1
16q23.1		 SLC35F1, C6orf204, PLN
GRID1
SLC25A46
WWOX		 rs89107-G
rs7910620-G
rs17132261-T
rs2059238-A		 0.50
0.01
0.02
0.22		 1 x 10-9 (LV internal diastolic dimensions)
7 x 10-7 (LV wall thickness)
9 x 10-7 (LV wall thickness)
3 x 10-6 (LV wall thickness)		 .03 [0.02-0.04] cm decrease
.17 [0.11-0.23] cm increase
.06 [0.04-0.08] cm increase
.02 [0.01-0.03] cm decrease		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
07/16/09 Bishop
July 05, 2009
Nat Genet
Genome-wide association study identifies three loci associated with melanoma risk. 		Melanoma 1,539 European ancestry cases, 3,917 European ancestry controls 2,312 European ancestry cases, 1,867 European ancestry controls 16q24.3
16q24.3
11q14.3
22q13.1
9p21.3		 MC1R
MC1R
TYR
Intergenic
CDKN2A		 rs258322-A
rs4785763-A
rs1393350-A
rs2284063-?
rs7023329-A		 0.09
0.32
0.27
0.37
0.50		 3 x 10-27
6 x 10-22
2 x 10-14
2 x 10-9
4 x 10-7 		1.67 [1.52-1.83]
1.36 [1.28-1.45]
1.29 [1.21-1.38]
1.2 [1.14-1.28]
1.18 [1.10-1.25]		 Illumina
[~317,000]		 N
07/13/09 Falchi
July 05, 2009
Nat Genet
Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi. 		Cutaneous nevi 1,524 European twins 4,107 European individuals 9p21.3
22q13.1		 MTAP
PLA2G6		 rs4636294-A
rs2284063-G		 0.48
0.35		 3 x 10-15
3 x 10-8 		.2 [0.13-0.27] increase in log nevus count
.08 [-0.002-0.16] decrease in log nevus count		 Illumina
[297,108]		 N
07/12/09 Shete
July 05, 2009
Nat Genet
Genome-wide association study identifies five susceptibility loci for glioma. 		Glioma 1,878 cases, 3,670 controls 2,545 cases, 2,953 controls 8q24.21
5p15.33
9p21.3
5p15.33
20q13.33
8q24.21
11q23.3		 CCDC26
TERT
CDKN2A, CDKN2B
TERT
RTEL1
CCDC26
PHLDB1		 rs4295627-G
rs2736100-G
rs4977756-G
rs2853676-A
rs6010620-G
rs891835-G
rs498872-T		 0.83
0.49
0.60
0.73
0.23
0.79
0.69		 2 x 10-18
2 x 10-17
7 x 10-15
4 x 10-14
3 x 10-12
8 x 10-11
1 x 10-8 		1.36 [1.29-1.43]
1.27 [1.19-1.37]
1.24 [1.19-1.30]
1.26 [1.20-1.32]
1.28 [1.21-1.35]
1.24 [1.17-1.30]
1.18 [1.13-1.24]		 Illumina
[454,576]		 N
07/12/09 Wrensch
July 05, 2009
Nat Genet
Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. 		Glioma (high-grade) 692 high-grade cases, 3,992 controls 176 high-grade cases, 174 controls 9p21.3
20q13.33
20q13.33		 Intergenic
RTEL1
RTEL1		 rs1412829-C
rs4809324-C
rs6010620-G		 0.39
0.10
0.77		 2 x 10-10
2 x 10-9
3 x 10-9 		1.42 [1.27-1.58]
1.6 [1.37-1.87]
1.52 [1.32-1.75]		 Illumina
[326,506]		 N
07/24/09 Teichert
July 04, 2009
Hum Mol Genet
A genome-wide association study of acenocoumarol maintenance dosage. 		Acenocoumarol maintenance dosage 1,451 Caucasian individuals 287 Caucasian individuals 10q23.33
19p13.12
10q23.33
3q22.3		 CYP2C18
CYP4F2
CYP2C19
CNTN4		 rs12772169-?
rs2108622-?
rs12767583-?
rs10935268-?		 NR
NR
NR
NR		 8 x 10-12
3 x 10-10
3 x 10-7
8 x 10-7 		NR
NR
NR
NR		 Illumina
[~550,000]		 N
07/12/09 Elliott
July 01, 2009
JAMA
Genetic Loci associated with C-reactive protein levels and risk of coronary heart disease. 		C-reactive protein 17,967 European and Indian Asian men and women 13,615 European and Indian Asian men and women 1q23.2
12q24.31
19q13.32
1q21.3
1p31.3		 CRP
HNF1A
APOE, APOC1, APOCII
IL6R
LEPR		 rs7553007-A
rs1183910-T
rs4420638-G
rs4537545-T
rs6700896-T		 NR
NR
NR
NR
NR		 8 x 10-44
1 x 10-30
5 x 10-27
2 x 10-14
3 x 10-14 		20.7 [18.9-23.4] % decrease
13.8 [10.9-16.6] % decrease
21.8 [18.1-25.3] % decrease
11.5 [8.5-14.4] % decrease
14.8 [12.0-17.6] % decrease		 Affymetrix, Illumina & Perlegen
[~1.4 million] (imputed)		 N
07/24/09 Estrada
July 01, 2009
Hum Mol Genet
A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide signaling pathway in the etiology of human height variation. 		Height 10,074 European individuals 6,912 European individuals 2q37.1
22q13.1
5p13.3
11q14.1
22q13.1		 DIS3L2, ALPP, NPPC
TNRC6B, ADSL
C5orf23, NPR3
TMEM126B, TMEM126A
SGSM3, MKL1		 rs6717918-T
rs139909-T
rs10472828-C
rs10898392-T
rs5757949-T		 0.78
0.68
0.56
NR
NR		 3 x 10-9
2 x 10-7
3 x 10-7
3 x 10-6
4 x 10-6 		.44 [0.20-0.68] cm increase
.25 [0.03-0.47] cm increase
.22 [0.04-0.40] cm increase
NR
NR		 Affymetrix, Illumina & Perlegen
[2,228,850] (imputed)		 N
07/13/09 International Schizophrenia Consortium
July 01, 2009
Nature
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder 		Schizophrenia 3,322 European descent cases, 3,587 European descent controls 4,692 European descent cases, 15,493 European descent controls 6p22.1
18q21.2
3q26.33
1p21.3		 MHC
TCF4
FXR1
PTBP2		 rs13194053-T
rs17594526-T
rs6782299-T
rs7544736-G		 0.86
0.03
0.73
0.18		 1 x 10-8
1 x 10-7
1 x 10-7
6 x 10-7 		1.22
1.44
1.1
1.25 		Affymetrix
[739,995]		 N
07/10/09 Shi
July 01, 2009
Nature
Common variants on chromosome 6p22.1 are associated with schizophrenia. 		Schizophrenia 2,681 European ancestry cases, 2,653 European ancestry controls, 1,286 African American cases, 973 African American controls 5,327 European ancestry cases, 16,424 European ancestry controls 6p22.1
6p21.32		 SLC17A1, SLC17A3, BTN3A2, BTN2A2, BTN3A1, HIST1H2AG, HIST1H2BJ, PRSS16, POM121L2, ZNF184
HLA-DQA1		 rs13194053-T
rs9272219-G		 0.82
0.72		 1 x 10-8 (EA)
7 x 10-8 (EA)		 1.28 [NR]
1.14 [NR]		 Affymetrix
[up to 843,798]		 N
07/10/09 Stefansson
July 01, 2009
Nature
Common variants conferring risk of schizophrenia. 		Schizophrenia 2,663 European cases, 13,498 European controls 10,282 European cases, 21,093 European controls 6p22.1
6p21.32
11q24.2
18q21.2
2p16.1
5q21.1
9q33.1		 MHC, PRSS16
MHC, NOTCH4
NRGN
TCF4
VRK2
SLCO6A1
Intergenic		 rs6932590-T
rs3131296-G
rs12807809-T
rs9960767-C
rs2312147-C
rs1502844-C
rs1572299-A		 0.78
0.87
0.83
0.06
NR
NR
NR		 1 x 10-12
2 x 10-10
2 x 10-9
4 x 10-9
3 x 10-7
1 x 10-6
4 x 10-6 		1.16 [NR]
1.19 [NR]
1.15 [NR]
1.23 [NR]
1.09 [NR]
1.09 [NR]
1.08 [NR]		 Illumina
[314,868]		 N
07/24/09 Treutlein
July 01, 2009
Arch Gen Psychiatry
Genome-wide association study of alcohol dependence. 		Alcohol dependence 476 German cases, 1,358 German controls 1,024 German cases, 996 German controls 2q35
5q32
Xp22.2
14q24.2
5q15
6q25.1		 PECR
PPP2R2B
Intergenic
Intergenic
CAST, ERAP1
ESR1		 rs7590720-G
rs1864982-A
rs12388359-T
rs36563-A
rs13160562-G
rs6902771-C		 0.29
0.13
0.11
0.15
0.68
0.51		 1 x 10-8
3 x 10-6
4 x 10-6
5 x 10-6
7 x 10-6
8 x 10-6 		1.35 [1.22-1.49]
1.36 [1.20-1.55]
1.61 [1.32-2.00]
1.33 [1.18-1.50]
1.27 [1.14-1.41]
1.24 [1.13-1.36]		 Illumina
[524,396]		 N
07/01/09 Thorleifsson
June 28, 2009
Nat Genet
Sequence variants in the CLDN14 gene associate with kidney stones and bone mineral density. 		Kidney stones 1,507 Icelandic cases, 34,033 Icelandic controls 1,520 Icelandic cases, 4,726 Icelandic controls, 746 Dutch cases, 3,751 Dutch controls 21q22.13 CLDN14 rs219780-C 0.79 4 x 10-12 1.25 [1.17-1.33] Illumina
[303,120]		 N
07/01/09 Heard-Costa
June 26, 2009
PLoS Genet
NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. 		Waist circumference 31,373 Caucasian individuals 38,641 Caucasian individuals 16q12.2
14q31.1
18q21.32
12q13.13
5p14.3
6p12.2
11p15.4		 FTO
NRXN3
MC4R
FAIM2, BCDIN3D
CDH12
PKHD1
OVCH2		 rs1558902-?
rs10146997-G
rs489693-?
rs7138803-?
rs4701252-?
rs1555967-?
rs7932813-?		 NR
NR
NR
NR
NR
NR
NR		 5 x 10-19
5 x 10-8
4 x 10-7
8 x 10-7
2 x 10-6
3 x 10-6
5 x 10-6 		NR
.65 [NR] cm increase
NR
NR
NR
NR
NR		 Affymetrix & Illumina
[up to 512,349]		 N
07/01/09 Lindgren
June 26, 2009
PLoS Genet
Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution. 		Adiposity 38,580 European-ancestry individuals Up to 102,064 European-ancestry individuals 6p12.3
8p23.1
1q41
1q42.3		 TFAP2B
MSRA
LYPLAL1
TBCE		 rs987237-G
rs7826222-G
rs2605100-G
rs6429082-C		 0.164
0.183
0.692
0.46		 2 x 10-11 (WC)
9 x 10-9 (WC)
3 x 10-8 (WHR in women)
3 x 10-7 (WC)		 .04 [0.03-0.05] z-score unit increase
.04 [0.03-0.05] z-score unit increase
.04 [0.03-0.05] z-score unit increase
NR		 Affymetrix & Illumina
[2,573,738] (imputed)		 N
07/01/09 Cotsapas
June 24, 2009
Hum Mol Genet
Common body mass index-associated variants confer risk of extreme obesity. 		Obesity (extreme) 775 Caucasian cases, 3,197 Caucasian controls NR 16q12.2
10p11.21
2p16.1
6p21.31
4q26
11p14.2
3p24.2
5q23.3
10q22.1
20p12.1
3p24.3
6p21.31
2q33.3		 FTO
ZNF248
RTN4
ITPR3
TRAM1L1
MUC15
RARB
FBN2
PRF1
C20orf133
RAFTLIN
MLN
FLJ20309		 rs9941349-T
rs7474896-T
rs6726292-G
rs999943-T
rs10433903-T
rs12295638-C
rs1435703-T
rs374748-G
rs10999409-T
rs6110577-C
rs12635698-C
rs2274459-A
rs7603514-A		 0.43
0.14
0.73
0.72
0.66
0.10
0.06
0.11
0.45
0.16
0.15
0.17
0.20		 6 x 10-12
9 x 10-7
1 x 10-6
1 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
8 x 10-6 		1.48 [1.33-1.66]
1.46 [1.25-1.69]
1.39 [1.22-1.59]
1.37 [1.20-1.56]
1.33 [1.19-1.52]
1.49 [1.26-1.77]
1.66 [1.34-2.06]
1.47 [1.25-1.73]
1.3 [1.16-1.45]
1.4 [1.21-1.61]
1.41 [1.21-1.63]
1.38 [1.20-1.58]
1.36 [1.19-1.56]		 Illumina
[457,251]		 N
06/30/09 Bahlo
June 14, 2009
Nat Genet
Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20. 		Multiple sclerosis 1,618 European ancestry cases, 3,413 European ancestry controls 2,256 European ancestry cases, 2,310 European ancestry controls 6p21.32
12q14.1
1p13.1
20q13.12
16p12.1
8q24.21
1p22.1
10p15.1		 HLA-DRB1
METTL1, CYP27B1
CD58
CD40
NR
ASAP1, DDEF1
EVI5, RPL5
IL2RA		 rs9271366-G
rs703842-A
rs1335532-A
rs6074022-G
rs8049603-T
rs6984045-C
rs6604026-G
rs2104286-A		 0.15
0.67
0.87
0.25
0.20
0.02
0.28
0.73		 7 x 10-184
5 x 10-11
1 x 10-7
1 x 10-7
1 x 10-6
2 x 10-6
3 x 10-6
7 x 10-6 		2.78 [NR]
1.23 [NR]
1.28 [NR]
1.2 [NR]
1.19 [NR]
1.59 [NR]
1.17 [NR]
1.16 [NR]		 Illumina
[302,098]		 N
06/29/09 De Jager
June 14, 2009
Nat Genet
Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. 		Multiple sclerosis 2,624 cases, 7,220 controls 2,215 cases, 2,116 controls 6p21.32
6p22.1
12p13.31
1p13.1
11q12.2
16q24.1
10p15.1
2q22.1
16p13.13
5p13.1
12q24.31
10q22.3
5p13.2
12p13.31
3q25.33		 HLA-DRB1
HLA-B
TNFRSF1A
CD58
CD6
IRF8
IL2RA
CXCR4
CLEC16A
PTGER4
MPHOSPH9
ZMIZ1
IL7R
TNFRSF1A
IL12A		 rs3135388-A
rs2523393-A
rs1800693-C
rs2300747-A
rs17824933-G
rs17445836-G
rs2104286-T
rs882300-C
rs11865121-C
rs6896969-C
rs1790100-G
rs1250540-G
rs6897932-C
rs4149584-T
rs4680534-C		 0.22
0.59
0.45
0.88
0.25
0.81
0.76
0.61
0.69
0.62
0.24
0.35
0.75
0.022
0.37		 4 x 10-225
1 x 10-17
2 x 10-11
3 x 10-10
4 x 10-9
4 x 10-9
9 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
7 x 10-7
2 x 10-6
2 x 10-6
5 x 10-6
6 x 10-6 		2.75 [2.46-3.07]
1.28 [1.18-1.39]
1.2 [1.10-1.31]
1.3 [1.14-1.47]
1.18 [1.07-1.30]
1.25 [1.12-1.39]
1.15 [1.04-1.27]
1.19 [1.09-1.30]
1.15 [1.04-1.25]
1.1 [1.01-1.20]
1.11 [1.00-1.22]
1.12 [1.02-1.22]
1.12 [1.02-1.23]
1.58 [1.15-2.17]
1.12 [1.02-1.22]		 Affymetrix & Illumina
[~2.56 million] (imputed)		 N
06/26/09 Malarstig
June 12, 2009
Blood
Identification of ZNF366 and PTPRD as novel determinants of plasma homocysteine in a family-based genome-wide association study 		Plasma homocysteine 387 individuals from 21 Spanish families 1,238 European individuals NS NS NS NS NS NS Illumina
[283,437]		 N
06/19/09 Knauff
June 09, 2009
Hum Reprod
Genome-wide association study in premature ovarian failure patients suggests ADAMTS19 as a possible candidate gene 		Premature ovarian failure 99 Caucasian cases, 235 Caucasian controls 60 Caucasian cases, 90 Caucasian controls NS NS NS NS NS NS Illumina
[309,158]		 N
06/19/09 Zhai
June 08, 2009
J Med Genet
A genome-wide association study suggests that a locus within the ataxin 2 binding protein 1 gene is associated with hand osteoarthritis: the Treat-OA consortium 		Osteoarthritis 1,804 Caucasian individuals 3,266 Caucasian individuals NS NS NS NS NS NS Illumina
[up to 535,188]		 N
06/17/09 Gregersen
June 07, 2009
Nat Genet
REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. 		Rheumatoid arthritis 2,418 cases, 4,504 controls 2,604 cases, 2,882 controls 1p13.2
2p16.1
2q33.2
8p23.1
9q33.2		 PTPN22
REL
CTLA4
BLK
TRAF1, C5		 rs2476601-?
rs13017599-A
rs231735-T
rs2736340-A
rs881375-?		 NR
0.34
0.51
0.24
NR		 2 x 10-21
2 x 10-12
6 x 10-9
6 x 10-9
4 x 10-8 		NR
1.21 [1.15-1.28]
1.17 [1.11-1.23]
1.19 [1.13-1.27]
NR		 Illumina
[278,502]		 N
06/17/09 Elmore
June 06, 2009
J Vasc Surg
Identification of a genetic variant associated with abdominal aortic aneurysms on chromosome 3p12.3 by genome wide association 		Abdominal aortic aneurysm 123 cases, 112 controls 827 cases, 594 controls NS NS NS NS NS NS Affymetrix
[306,330] (pooled)		 N
06/22/09 Kolz
June 05, 2009
PLoS Genet
Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations. 		Serum uric acid 12,328 European males, 15,813 European females NR 4p16.1
4p16.1
4q22.1
6p22.2
11q13.1
4q22.1
2p23.3
11q13.1
1q21.1
6p22.2
10q21.1		 SLC2A9
SLC2A9
ABCG2
SLC17A1
SLC22A11
ABCG2
GCKR
SLC22A12
PDZK1
LRRC16A, SCGN
SLC16A9		 rs734553-T
rs734553-T
rs2231142-T
rs1183201-A
rs17300741-A
rs2231142-T
rs780094-T
rs505802-T
rs12129861-A
rs742132-A
rs12356193-A		 0.77
0.77
0.11
0.48
0.51
0.11
0.42
0.70
0.46
0.70
0.83		 1 x 10-192 (women)
1 x 10-41 (men)
2 x 10-18 (men)
3 x 10-14
7 x 10-14
1 x 10-10 (women)
1 x 10-9
2 x 10-9
3 x 10-9
9 x 10-9
1 x 10-8 		.4 [0.371-0.423] mg/dl increase
.22 [0.188-0.252] mg/dl increase
.22 [0.171-0.270] mg/dl increase
.06 [0.459-0.078] mg/dl decrease
.06 [0.046-0.078] mg/dl increase
.14 [0.096-0.181] mg/dl increase
.05 [0.035-0.068] mg/dl increase
.06 [0.038-0.074] mg/dl decrease
.06 [0.042-0.083] mg/dl decrease
.05 [0.036-0.072] mg/dl increase
.08 [0.051-0.105] mg/dl increase		 Affymetrix and Illumina
[2,493,963] (imputed)		 N
06/16/09 Smith
June 02, 2009
Mol Psychiatry
Genome-wide association study of bipolar disorder in European American and African American individuals. 		Bipolar disorder 1,001 Caucasian cases, 345 African American cases, 1,033 Caucasian controls, 670 African American controls 1,749 Caucasian family members, 1,263 Caucasian cases, 431 Caucasian controls 19q13.11 DPY19L3 rs2111504-T 0.23 2 x 10-6 (AA) 1.74 [NR] Affymetrix
[702,044]		 N
06/15/09 Daly
May 31, 2009
Nat Genet
HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. 		Drug-induced liver injury (flucloxacillin) 58 cases, 282 controls NR 6p21.33
3q27.3
3q11.2
12q12
9p21.2
15q26.2		 HCP5, HLA-B
ST6GAL1
OR5H2
ALG10B
C9org82
MCTP2		 rs2395029-?
rs10937275-?
rs1497546-?
rs6582630-?
rs10812428-?
rs4984390-?		 0.05
0.09
0.02
0.38
0.31
0.41		 9 x 10-33
1 x 10-8 (B*5701 positive)
2 x 10-7
1 x 10-6
1 x 10-6
4 x 10-6 		45 [19.4-105]
4.1 [NR]
6.57 [NR]
2.82 [NR]
2.85 [NR]
3.27 [NR]		 Illumina
[866,399]		 N
06/14/09 Kanetsky
May 31, 2009
Nat Genet
Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer. 		Testicular cancer 277 white, non-Hispanic cases, 919 non-Hispanic controls 371 non-Hispanic cases + 204 sets of parents, 860 non-Hispanic controls 12q21.32 KITLG rs4474514-A NR 6 x 10-15 3.07 [2.29-4.13] Affymetrix
[611,254]		 N
06/14/09 Rapley
May 31, 2009
Nat Genet
A genome-wide association study of testicular germ cell tumor. 		Testicular germ cell tumor 730 cases, 1,435 controls 571 cases, 1,806 controls 12q21.32
12q21.32
6p21.31
5q31.3
4q24
1q24.1		 KITLG
KITLG
BAK1
SPRY4
Intergenic
Intergenic		 rs995030-G
rs1508595-G
rs210138-G
rs4624820-A
rs4699052-C
rs4657482-A		 0.80
0.83
0.20
0.54
0.61
0.33		 1 x 10-31
3 x 10-30
1 x 10-13
3 x 10-13
2 x 10-7
2 x 10-6 		2.55 [2.05-3.19]
2.69 [2.10-3.44]
1.5 [1.28-1.75]
1.37 [1.19-1.58]
1.21 [1.05-1.39]
1.14 [0.99-1.31]		 Illumina
[307,666]		 N
06/14/09 Ng
May 29, 2009
J Hum Genet
A genome-wide association study identifies ITGA9 conferring risk of nasopharyngeal carcinoma. 		Nasopharyngeal carcinoma 111 Chinese cases, 260 Chinese controls 168 Chinese cases, 252 Chinese controls 3p22.2 ITGA9 rs189897-A 0.09 7 x 10-8 3.18 [1.94-5.21] Illumina
[533,048]		 N
06/16/09 Aston
May 28, 2009
J Androl
Genome-wide study of single-nucleotide polymorphisms associated with azoospermia and severe oligozoospermia. 		Male infertility 52 oligozoospermic Caucasian males, 40 non-obstructive azoospermic Caucasian males, 80 Caucasian male controls NR 12p12.2
20q13.2
3q11.2
2q22.1
12p13.32		 PDE3A
SALL4
ARL6
NXPH2
EFCAB4B		 rs10841496-?
rs6068020-?
rs9814870-?
rs1399645-?
rs10848911-?		 0.58
0.49
0.15
0.02
0.11		 5 x 10-7 (azoospermia)
5 x 10-7 (azoospermia)
7 x 10-7 (oligozoospermia)
9 x 10-7 (azoospermia)
4 x 10-6 (azoospermia)		 NR
NR
NR
NR
NR		 Illumina
[314,776]		 N
06/10/09 Ma
May 28, 2009
Ann Hum Genet
A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. 		Autism 1,390 family members 2,390 family members 5p14.1 Intergenic rs10038113-T 0.59 3 x 10-6 1.33 [1.11-1.43] Illumina
[775,311]		 N
06/14/09 Jallow
May 24, 2009
Nat Genet
Genome-wide and fine-resolution association analysis of malaria in West Africa. 		Malaria 958 Gambian cases, 1,382 Gambian controls, all children 1,087 Gambian cases, 2,376 Gambian controls, all children 11p15.4
17p13.1
7p12.2		 HBB
SCO1
DDC		 rs11036238-?
rs6503319-T
rs1451375-?		 0.14
0.45
0.78		 4 x 10-11
7 x 10-7
6 x 10-6 		1.59 [1.39-1.82]
1.21 [1.12-1.31]
1.33 [1.18-1.52]		 Affymetrix
[402,814]		 N
06/04/09 Norris
May 21, 2009
Obesity (Silver Spring)
Genome-wide Association Study and Follow-up Analysis of Adiposity Traits in Hispanic Americans: The IRAS Family Study 		Obesity-related traits 229 Hispanic family members 961 Hispanic family members NS NS NS NS NS NS Illumina
[309,200]		 N
06/21/09 Hirschfield
May 20, 2009
N Engl J Med
Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. 		Primary biliary cirrhosis 505 cases, 1,507 controls up to 526 cases, 1,206 controls 3q26.1
1p31.3
6p21.32
6p21.32
7q32.1
3q26.1
17q12		 IL12A
IL12RB2
c6orf10, BTNL2, HLA-DQB1
c6orf10, BTNL2, HLA-DQB1
IRF5-TNPO3
ARF7
IKZF3		 rs6441286-G
rs3790567-A
4-SNP haplotype-1
4-SNP haplotype-2
rs10488631-G
rs4679904-G
rs907092-A		 0.39
0.24
0.01
0.20
NR
0.72
0.45		 2 x 10-14
3 x 10-11
1 x 10-10 (AACA)
7 x 10-10 (CACA)
2 x 10-7
1 x 10-6
8 x 10-6 		1.54 [1.38-1.72]
1.51 [1.33-1.70]
NR
NR
1.52 [1.30-1.78]
1.38 [1.21-1.57]
1.29 [1.15-1.44]		 Illumina
[305,724]		 N
06/14/09 Arnett
May 19, 2009
BMC Med Genet
Genome-wide association study identifies single-nucleotide polymorphism in KCNB1 associated with left ventricular mass in humans: the HyperGEN Study. 		Left ventricular mass 101 Caucasian cases, 101 Caucasian controls 704 Caucasian siblings, 1,467 African American siblings 5p13.2
7q21.11		 RAI14
CD36		 rs409045-?
rs10499859-?		 0.38
0.45		 8 x 10-7 (Caucasian)
3 x 10-6 (Caucasian)		 0 [NR] (LVMI)
.09 [NR] (LVMI)		 Affymetrix
[96,258]		 N
06/04/09 Landers
May 18, 2009
Proc Natl Acad Sci U S A
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis. 		Amyotrophic lateral sclerosis 1,821 cases, 2,258 controls 538 cases, 556 controls 1q24.2
7q36.1
18q12.1
2p16.1
5q23.2
1q24.2
6p22.3
2q24.3
3p26.3
17q24.3
1p34.2
1q42.2
2p22.1
5q23.1
21q21.1
2q24.2		 KIFAP3
ZNF746
B4GALT6
EFEMP1
CSNK1G3
SELL
ATXN1
SCN7A
CNTN4
SLC39A11
NT5C1A
DISC1
NR
SEMA6A
NR
RBMS1		 rs1541160-C
rs855913-A
rs10438933-G
rs7577894-T
rs11241713-T
rs3177980-G
rs697739-A
rs13015447-G
rs2619566-G
rs8066857-C
rs873917-T
rs16856202-C
rs3099950-?
rs7702057-A
rs2823962-?
rs10192369-T		 NR
NR
0.12
0.39
NR
NR
NR
0.34
NR
NR
0.29
0.04
NR
0.03
NR
0.47		 2 x 10-8 (survival)
4 x 10-8 (survival)
1 x 10-6 (susceptibilty)
1 x 10-6 (site of onset)
3 x 10-6 (survival)
4 x 10-6 (survival)
4 x 10-6 (age of onset)
7 x 10-6 (site of onset)
7 x 10-6 (age of onset)
8 x 10-6 (site of onset)
8 x 10-6 (susceptibilty)
8 x 10-6 (susceptibilty)
8 x 10-6 (survival)
8 x 10-6 (site of onset)
9 x 10-6 (survival)
9 x 10-6 (susceptibilty)		 .58 [0.38-0.78] years older
1.08 [0.70-1.46] years older
1.3 [NR]
1.41 [NR]
.79 [0.46-1.12] years older
.51 [0.46-0.56] years older
2.04 [1.18-2.90] years younger
1.41 [NR]
3.03 [1.71-4.35] years younger
1.48 [NR]
1.16 [NR]
2 [NR]
NR
2.05 [NR]
NR
1.17 [NR]		 Illumina
[288,357]		 N
06/04/09 He
May 17, 2009
Nat Genet
Genome-wide association studies identify loci associated with age at menarche and age at natural menopause. 		Menarche and menopause (age at onset) 17,438 Caucasian women NR 20p12.3
19q13.42
5q35.2
6q21
9q31.2
6p24.2		 TRMT6, MCM8
BRSK1
UIMC1
LIN28B
Intergenic
GCM2, SYCP2L		 rs16991615-A
rs1172822-T
rs365132-T
rs314277-A
rs7861820-C
rs2153157-T		 0.06
0.37
0.49
0.14
0.48
0.49		 1 x 10-21 (age at natural menopause)
2 x 10-19 (age at natural menopause)
8 x 10-14 (age at natural menopause)
3 x 10-13 (age at menarche)
3 x 10-9 (age at menarche)
5 x 10-8 (age at natural menopause)		 1.07 [0.85-1.29] years older
.49 [0.38-0.60] years younger
.39 [0.29-0.49] years older
.16 [0.12-0.20] years older
.09 [0.06-0.12] years younger
.29 [0.19-0.39] years older		 Illumina
[317,759]		 N
06/01/09 Ong
May 17, 2009
Nat Genet
Genetic variation in LIN28B is associated with the timing of puberty. 		Menarche (age at onset) 4,714 women 16,373 women 6q21 LIN28B rs314276-C 0.67 4 x 10-16 .14 [0.11-0.17] years younger Affymetrix
[up to 390,631]		 N
05/28/09 Perry
May 17, 2009
Nat Genet
Meta-analysis of genome-wide association data identifies two loci influencing age at menarche. 		Menarche (age at onset) 17,510 women NR 9q31.2
6q21		 TMEM38B, SLC44A1, FKTN, FSD1L, TAL2, ZNF462
LIN28B		 rs2090409-A
rs7759938-C		 0.31
0.33		 2 x 10-9
7 x 10-9 		.1 [0.06-0.14] years younger
.09 [0.05-0.13] years older		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
06/01/09 Perlis
May 15, 2009
Am J Psychiatry
A Genomewide Association Study of Response to Lithium for Prevention of Recurrence in Bipolar Disorder 		Response to lithium treatment in bipolar disorder 458 lithium-treated subjects, 719 non-lithium treated subjects 359 subjects NS NS NS NS NS NS Affymetrix
[~1.4 million] (imputed)		 N
05/28/09 Stolk
May 15, 2009
Nat Genet
Loci at chromosomes 13, 19 and 20 influence age at natural menopause. 		Menopause (age at onset) 2,979 women 2,560 women 19q13.42
20p12.3
13q34
9q21.31
16q24.2
11q25
8p12
7q22.3
6p21.32
3q26.2
20p12.3
2q23.3
14q32.31		 BRSK1, TMEM224, SUV420H2
MCM8
LOC121793, ARHGEF7
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 rs1172822-T
rs236114-A
rs7333181-A
rs2151145-?
rs4843747-?
rs4397868-?
rs6468442-?
rs17153527-?
rs494620-?
rs4955755-?
rs2326679-?
rs11889862-?
rs4906172-?		 0.39
0.21
0.12
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 6 x 10-11
1 x 10-10
3 x 10-8
1 x 10-7
2 x 10-7
3 x 10-7
3 x 10-7
4 x 10-7
5 x 10-7
7 x 10-7
2 x 10-6
2 x 10-6
3 x 10-6 		.39 [0.27-0.51] years younger
.5 [0.34-0.65] years older
.52 [0.34-0.70] years older
.41 [0.26-0.56] years older
.39 [0.24-0.54] years older
.4 [0.25-0.55] years younger
.39 [0.24-0.54] years younger
.51 [0.31-0.71] years older
.3 [0.18-0.42] years older
.34 [0.21-0.47] years older
.32 [0.19-0.45] years older
.36 [0.21-0.51] years younger
.36 [0.21-0.51] years younger		 Illumina
[315,418]		 N
06/01/09 Sulem
May 15, 2009
Nat Genet
Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche. 		Menarche (age at onset) 15,297 Icelandic women 10,040 Icelandic women 6q21 LIN28B, HACE1, E3 ubiquitin protein ligase 1, BVES, POPDC3 rs314280-T 0.48 2 x 10-14 1.2 [0.9-1.5] months older Illumina
[304,226]		 N
05/26/09 Fei
May 14, 2009
Arthritis Res Ther
Identification of novel genetic susceptibility loci for Behcet's disease using a genome-wide association study 		Behcet's disease 152 cases, 170 controls NR NS NS NS NS NS NS Affymetrix
[~500,000] (pooled)		 N
06/01/09 Barrett
May 10, 2009
Nat Genet
Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. 		Type 1 diabetes 7,514 cases, 9,045 controls 4,267 cases, 4,670 controls, 4,342 trios 6p21.32
1p13.2
11p15.5
10q23.31
12q24.12
12q13.2
16p13.13
22q12.2
2q33.2
16q23.1
18p11.21
10p15.1
16p11.2
6q22.32
4q27
17q12
14q24.1
9p24.2
20p13
12p13.31
19q13.32
4p15.2
17q21.2
1q32.1
21q22.3
14q32.2
7p15.2
2q24.2
Xq28
7p12.1
6q15
15q25.1
10p15.1
16p12.3
22q13.1
1p31.3
17p13.1
2p25.1		 MHC
PTPN22
INS
C10orf59
SH2B3
ERBB3
CLEC16A
Intergenic
CTLA4
Intergenic
PTPN2
IL2RA
IL27
C6orf173
IL2
ORMDL3
Intergenic
GLIS3
Intergenic
CD69
Intergenic
Intergenic
Intergenic
IL10
UBASH3A
Intergenic
Intergenic
IFIH1
Intergenic
COBL
BACH2
CTSH
PRKCQ
Intergenic
C1QTNF6
PGM1
Intergenic
Intergenic		 rs9268645-?
rs2476601-?
rs7111341-?
rs10509540-?
rs3184504-?
rs2292239-?
rs12708716-?
rs5753037-T
rs3087243-?
rs7202877-G
rs1893217-?
rs12251307-?
rs4788084-G
rs9388489-G
rs4505848-?
rs2290400-?
rs1465788-?
rs7020673-?
rs2281808-?
rs4763879-A
rs425105-?
rs10517086-A
rs7221109-?
rs3024505-?
rs11203203-?
rs4900384-G
rs7804356-?
rs1990760-?
rs2664170-G
rs4948088-?
rs11755527-?
rs3825932-?
rs11258747-?
rs12444268-A
rs229541-?
rs2269241-G
rs16956936-?
rs1534422-G		 NR
NR
NR
0.71
NR
NR
NR
0.39
NR
0.10
NR
NR
0.42
0.45
NR
0.50
0.71
0.50
0.64
0.37
0.84
0.30
0.65
0.83
NR
0.29
0.76
NR
0.32
0.95
NR
NR
NR
0.30
NR
0.19
0.86
0.46		 1 x 10-100
9 x 10-85
4 x 10-48
1 x 10-28
3 x 10-27
2 x 10-25
2 x 10-16
3 x 10-16
1 x 10-15
3 x 10-15
4 x 10-15
1 x 10-13
3 x 10-13
4 x 10-13
5 x 10-13
6 x 10-13
2 x 10-12
5 x 10-12
1 x 10-11
2 x 10-11
3 x 10-11
5 x 10-10
1 x 10-9
2 x 10-9
2 x 10-9
4 x 10-9
5 x 10-9
7 x 10-9
8 x 10-9
4 x 10-8
5 x 10-8
8 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
4 x 10-7
5 x 10-7
2 x 10-6 		NR
NR
NR
1.33 [1.25-1.43]
NR
NR
NR
1.1 [1.04-1.17]
NR
1.28 [1.17-1.41]
NR
NR
1.09 [1.02-1.16]
1.17 [1.10-1.24]
NR
1.15 [1.08-1.22]
1.16 [1.10-1.25]
1.14 [1.08-1.20]
1.11 [1.05-1.19]
1.09 [1.02-1.16]
1.16 [1.08-1.27]
1.09 [1.02-1.17]
1.05 [0.99-1.12]
1.19 [1.10-1.30]
NR
1.09 [1.02-1.16]
1.14 [1.06-1.22]
NR
1.16 [1.07-1.24]
1.3 [1.11-1.49]
NR
NR
NR
1.1 [1.03-1.17]
NR
1.1 [1.02-1.18]
1.09 [1.00-1.19]
1.08 [1.02-1.15]		 Affymetrix & Illumina
[841,622] (imputed)		 N
05/27/09 Kottgen
May 10, 2009
Nat Genet
Multiple loci associated with indices of renal function and chronic kidney disease. 		Renal function and chronic kidney disease 19,877 individuals, up to 2,388 cases 21,466 individuals, up to 1,932 cases 16p12.3
15q21.1
4q21.1
16p12.3		 UMOD
SPATA5L1, GATM
SHROOM3
UMOD		 rs12917707-T
rs2467853-G
rs17319721-A
rs12917707-G		 0.18
0.38
0.44
0.82		 5 x 10-16 (eGFRcrea)
6 x 10-14 (eGFRcrea)
1 x 10-12 (eGFRcrea)
2 x 10-12 (CKD)		 .02 [0.014-0.022] ml/min/1.73m2 increase
.01 [0.009-0.017] ml/min/1.73m2 decrease
.01 [0.008-0.016] ml/min/1.73m2 decrease
1.25 [1.18-1.33]		 Affymetrix & Illumina
[~2.5 million] (imputed)		 N
05/19/09 Levy
May 10, 2009
Nat Genet
Genome-wide association study of blood pressure and hypertension. 		Diastolic blood pressure 29,136 individuals 34,433 individuals 12q24.12
15q24.1
12q21.33
3p22.1
10p12.33
12q24.21
11p15.1		 SH2B3
CSK, ULK3
ATP2B1
ULK4
CACNB2
TBX3, TBX5
PLEKHA7		 rs3184504-T
rs6495122-A
rs2681472-A
rs9815354-A
rs11014166-A
rs2384550-A
rs11024074-T		 0.48
0.42
0.83
0.17
0.66
0.35
0.72		 3 x 10-14
2 x 10-10
1 x 10-9
3 x 10-9
1 x 10-8
4 x 10-8
1 x 10-6 		.48 [0.36-0.60] mm Hg increase
.4 [0.28-0.52] mm Hg increase
.5 [0.34-0.66] mm Hg increase
.49 [0.33-0.65] mm Hg increase
.37 [0.25-0.49] mm Hg increase
.35 [0.23-0.47] mm Hg decrease
.33 [0.19-0.47] mm Hg decrease		 Affymetrix & Illumina
[2,533,153](imputed)		 N
05/19/09 " Hypertension 29,136 individuals 34,433 individuals 12q21.33
10p12.33
20q13.32
8p23.1		 ATP2B1
CACNB2
ZNF831, EDN3
MSRA		 rs2681472-A
rs11014166-A
rs16982520-A
rs11775334-A		 0.83
0.66
0.88
0.32		 2 x 10-11
6 x 10-8
2 x 10-7
4 x 10-6 		.15 [0.11-0.19] increase in log odds
.09 [0.05-0.13] increase in log odds
.13 [0.09-0.17] decrease in log odds
.08 [0.04-0.12] increase in log odds		 Affymetrix & Illumina
[2,533,153](imputed)		 N
05/19/09 " Systolic blood pressure 29,136 individuals 34,433 individuals 12q21.33
10q24.32
11p15.1
12q24.12
3q26.2
10p12.33
1p36.22		 ATP2B1
CYP17A1
PLEKHA7
SH2B3
MDS1
CACNB2
CASZ1		 rs2681492-T
rs1004467-A
rs381815-T
rs3184504-T
rs448378-A
rs11014166-A
rs12046278-T		 0.80
0.90
0.26
0.48
0.52
0.66
0.64		 4 x 10-11
1 x 10-10
2 x 10-9
5 x 10-9
1 x 10-7
7 x 10-7
5 x 10-6 		.85 [0.60-1.10] mm Hg increase
1.05 [0.74-1.36] mm Hg increase
.65 [0.43-0.87] mm Hg increase
.58 [0.38-0.78] mm Hg increase
.51 [0.31-0.71] mm Hg decrease
.5 [0.30-0.70] mm Hg increase
.53 [0.29-0.77] mm Hg decrease		 Affymetrix & Illumina
[2,533,153](imputed)		 N
05/19/09 Newton-Cheh
May 10, 2009
Nat Genet
Genome-wide association study identifies eight loci associated with blood pressure. 		Diastolic blood pressure 34,433 individuals Up to 100,347 white individuals, up to 12,889 Indian Asian individuals 15q24.1
4q21.21
12q24.12
10q21.2
17q21.32
3q26.2		 CYP1A1, CYP1A2, CSK, LMAN1L, CPLX3, ARID3B
FGF5, PRDM8, c4orf22
ATXN2, SH2B3
c10orf107, TMEM26, RTKN2, RHOBTB1, ARID5B
ZNF652, PHB
MDS1		 rs1378942-C
rs16998073-T
rs653178-T
rs1530440-T
rs16948048-G
rs1918974-T		 0.36
0.21
0.53
0.19
0.39
0.54		 1 x 10-23
1 x 10-21
3 x 10-18
1 x 10-9
5 x 10-9
8 x 10-8 		.43 [0.35-0.51] mm Hg increase
.5 [0.40-0.60] mm Hg increase
.46 [0.36-0.56] mm Hg decrease
.39 [0.27-0.51] mm Hg decrease
.31 [0.21-0.41] mm Hg increase
.27 [0.17-0.37] mm Hg decrease		 Affymetrix & Illumina
[2,497,993] (imputed)		 N
05/19/09 " Systolic blood pressure 34,433 individuals Up to 100,347 white individuals, up to 12,889 Indian Asian individuals 10q24.32
1p36.22
17q21.31		 CYP17A1, AS3MT, CNNM2, NT5C2
MTHFR, NPPA, CLCN6, NPPB, AGTRAP
PLCD3, ACBD4, HEXIM1, HEXIM2		 rs11191548-T
rs17367504-G
rs12946454-T		 0.91
0.14
0.28		 7 x 10-24
2 x 10-13
1 x 10-8 		1.16 [0.92-1.40] mm Hg increase
.85 [0.63-1.07] mm Hg decrease
.57 [0.37-0.77] mm Hg increase		 Affymetrix & Illumina
[2,497,993] (imputed)		 N
05/21/09 Rich
May 09, 2009
Diabetologia
A genome-wide association scan for acute insulin response to glucose in Hispanic-Americans: the Insulin Resistance Atherosclerosis Family Study (IRAS FS). 		Insulin response 229 family members 961 family members NS NS NS NS NS NS Illumina
[309,200]		 N
05/20/09 Himes
May 07, 2009
Am J Hum Genet
Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. 		Asthma 422 cases, 1,533 controls 3,750 white cases, 13,365 white controls, 592 white trios, 1,903 black cases, 2,432 black controls, 929 black family members 5q12.1 PDE4D rs1588265-C 0.29 3 x 10-8 1.18 [1.08-1.30] Illumina
[518,230]		 N
05/21/09 Yang
May 07, 2009
PLoS ONE
Genome-wide association study of young-onset hypertension in the Han Chinese population of Taiwan 		Hypertension (young onset) 175 Han Chinese cases, 175 Han Chinese controls 833 Han Chinese cases, 833 Han Chinese controls 2p22.3 LOC344371, MYADML, FAM98A, RASGRP3 4-SNP-haplotype NR 3 x 10-10 NR Affymetrix
[91,713]		 N
05/19/09 Sanna
May 06, 2009
Hum Mol Genet
Common variants in the SLCO1B3 locus are associated with bilirubin levels and unconjugated hyperbilirubinemia. 		Bilirubin levels 4,300 individuals 2,692 individuals 2q37.1
12p12.2
Xq28		 UGT1A1
SLC01B3
G6PD		 rs887829-T
rs2117032-C
rs766420-G		 0.30
0.47
0.18		 1 x 10-69
3 x 10-14
9 x 10-9 		.57 [0.50-0.63] s.d. decrease
.13 [0.08-0.18] s.d. increase
.18 [0.12-0.24] s.d. decrease		 Affymetrix
[362,129]		 N
05/14/09 Scott
May 05, 2009
Proc Natl Acad Sci U S A
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry. 		Bipolar disorder 3,683 cases, 14,507 controls NR 5q15
1p32.1
3p21.1
11q13.1
19p13.3
2p12
2q11.2
4q12
3q26.1
8p12
9q34.13
15q23
17q21.33		 MCTP1
NF1A
ITIH1, NEK4
NR
NR
CTNNA2
Intergenic
KIT
NR
NR
NR
NR
NR		 rs17418283-C
rs472913-C
rs1042779-A
rs2242663-T
rs7250872-T
rs13409348-G
rs6733011-G
rs2537859-T
rs7427021-G
rs6990255-T
rs2905072-A
rs6494849-A
rs1035050-T		 0.28
0.50
0.63
0.25
0.69
0.24
0.46
0.60
0.56
0.95
0.77
0.12
0.40		 1 x 10-7
2 x 10-7
2 x 10-7
1 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
9 x 10-6 		1.21 [1.13-1.30]
1.18 [1.11-1.25]
1.19 [1.11-1.27]
1.2 [1.11-1.29]
1.21 [1.12-1.31]
1.2 [1.11-1.29]
1.17 [1.10-1.25]
1.16 [1.09-1.24]
1.16 [1.09-1.24]
1.33 [1.18-1.51]
1.21 [1.11-1.32]
1.23 [1.13-1.35]
1.17 [1.09-1.25]		 Affymetrix and Illumina
[2,366,197] (imputed)		 N
05/12/09 Johnson
May 04, 2009
Hum Mol Genet
Genome-wide association meta-analysis for total serum bilirubin levels. 		Serum bilirubin levels 9,264 individuals NR 2q37.1
12p12.1
11p15.4
2p11.2
6p22.1
4q28.1
7q21.11
13q34		 UGT1A1
SLCO1B1,LST-3TM12,SLCO1A2
SLC22A18
KRCC1
HIST1H2BC
Intergenic
SEMA3C
ARHGEF7		 rs6742078-T
rs4149056-C
rs16928809-A
rs12714207-T
rs12206204-T
rs1986655-A
rs4236644-A
rs4773330-A		 0.32
0.15
0.09
0.32
0.02
0.17
0.26
0.12		 5 x 10-324
7 x 10-13
1 x 10-7
5 x 10-7
8 x 10-7
2 x 10-6
2 x 10-6
8 x 10-6 		.23 [0.21-0.25] umol/l increase in log(tbil)
.05 [0.03-0.07] umol/l increase in log(tbil)
.06 [0.04-0.08] umol/l increase in log(tbil)
.03 [0.01-0.05] umol/l decrease in log(tbil)
.18 [0.10-0.26] umol/l increase in log(tbil)
.02 [0.00-0.04] umol/l decrease in log(tbil)
.02 [0.00-0.04] umol/l decrease in log(tbil)
.04 [0.02-0.06] umol/l decrease in log(tbil)		 Affymetrix & Illumina
[2,555,103] (imputed)		 N
05/07/09 Capasso
May 03, 2009
Nat Genet
Common variations in BARD1 influence susceptibility to high-risk neuroblastoma. 		Neuroblastoma (high-risk) 397 cases, 2,043 controls 189 cases, 1,178 controls 2q35 BARD1 rs6435862-G 0.29 9 x 10-18 1.68 [1.49-1.90] Illumina
[462,866]		 N
05/07/09 Hallmayer
May 03, 2009
Nat Genet
Narcolepsy is strongly associated with the T-cell receptor alpha locus. 		Narcolepsy 807 Caucasian cases, 1,074 Caucasian controls 363 Caucasian cases, 355 Caucasian controls, 561 Asian cases, 605 Asian controls, 133 African American cases, 144 African American controls 14q11.2 TRA-alpha, TRAJ10 rs1154155-C 0.14 3 x 10-22 1.69 [1.52-1.88] Affymetrix
[549,596]		 N
05/07/09 Takeuchi
April 29, 2009
Diabetes
Confirmation of multiple risk Loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population. 		Type 2 diabetes 519 Japanese cases, 503 Japanese controls 5,629 Japanese cases, 7,370 Japanese controls 9p21.3
11p15.5
6p22.3
8q24.11
10q23.33
10q25.2
3q27.2		 CDKN2A, CDKN2B
KCNQ1
CDKAL1
SLC30A8
HHEX
TCF7L2
IGF2BP2		 rs2383208-A
rs2237892-C
rs4712523-G
rs13266634-C
rs1111875-C
rs7903146-T
rs4402960-T		 0.55
0.59
0.41
0.57
0.28
0.04
0.31		 2 x 10-29
1 x 10-26
7 x 10-20
2 x 10-14
7 x 10-12
8 x 10-12
1 x 10-6 		1.34 [1.27-1.41]
1.33 [1.27-1.41]
1.27 [1.21-1.33]
1.22 [1.16-1.28]
1.21 [1.15-1.28]
1.54 [1.36-1.74]
1.14 [1.08-1.21]		 Illumina
[482,625]		 N
05/11/09 Wang
April 28, 2009
Nature
Common genetic variants on 5p14.1 associate with autism spectrum disorders. 		Autism 3,101 family members, 1,204 cases, 6,491 controls 1,390 family members, 108 cases, 540 controls 5p14.1 CDH10,CDH9 rs4307059-T 0.61 2 x 10-10 1.19 [NR] Illumina
[474,019]		 N
05/05/09 Cho
April 26, 2009
Nat Genet
A large-scale genome-wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits. 		Biomedical quantitative traits 8,842 Korean individuals 7,861 Korean individuals 12q24.13
7q31.31
6q22.31
1q32.2
12q21.33
16q12.2
7q31.31
12q21.33		 C12orf51
FAM3C
LOC644502
CD46, LOC148696
ATP2B1
FTO
FAM3C
ATP2B1		 rs2074356-T
rs7776725-C
rs12110693-A
rs12731740-T
rs17249754-A
rs9939609-A
rs7776725-C
rs17249754-A		 0.15
0.13
0.49
0.10
0.37
0.13
0.13
0.37		 8 x 10-12 (waist-hip ratio)
1 x 10-11 (BD-RT)
2 x 10-9 (pulse rate)
3 x 10-9 (pulse rate)
1 x 10-7 (SBP)
2 x 10-7 (BMI)
2 x 10-6 (BD-TT)
3 x 10-6 (DBP)		 .01 [0.004-0.008] decrease
NR
.66 [0.45-0.87] beats per minute increase
1.09 [0.72-1.44] beats per minute increase
1.06 [0.67-1.45] mm Hg decrease
.24 [0.14-0.32] kg/m2 increase
NR
.63 [0.37-0.89] mm Hg decrease		 Affymetrix
[2,156,535] (imputed)		 N
05/05/09 " Height 8,842 Korean individuals 7,861 Korean individuals 3q23
8q12.1
2p16.1
6p21.31
1p12		 ZBTB38
PLAG1
EFEMP1
HMGA1
Intergenic		 rs10513137-A
rs13273123-G
rs3791675-G
rs6918981-G
rs17038182-C		 0.26
0.07
0.22
0.21
0.42		 6 x 10-12
1 x 10-9
2 x 10-9
3 x 10-8
5 x 10-7 		.46 [0.33-0.59] cm increase
.71 [0.48-0.94] cm decrease
.42 [0.28-0.56] cm increase
.4 [0.26-0.54] cm increase
.3 [0.18-0.42] cm decrease		 Affymetrix
[2,156,535] (imputed)		 N
04/23/09 Ikram
April 15, 2009
N Engl J Med
Genomewide association studies of stroke. 		Stroke 19,602 Caucasian individuals 3,004 African American individuals, 652 Caucasian cases, 3,613 Caucasian controls 12p13.33 NINJ2 rs12425791-A 0.19 1 x 10-9 (ischemic stroke) 1.29 [1.19-1.41] Affymetrix & Illumina
[2,194,468]		 N
04/22/09 Poduslo
April 14, 2009
Am J Med Genet B Neuropsychiatr Genet
A genome screen of successful aging without cognitive decline identifies LRP1B by haplotype analysis. 		Aging 89 cases, 227 controls NR 2q22.1 LRP1B rs12474609-? NR 6 x 10-9 NR Affymetrix
[469,218]		 N
05/05/09 Hiura
April 10, 2009
Circ J
Identification of genetic markers associated with high-density lipoprotein-cholesterol by genome-wide screening in a Japanese population: the Suita study. 		LDL cholesterol 900 Japanese individuals 1,810 Japanese individuals 16q13 CETP rs3764261-A 0.20 3 x 10-12 6.2 mg/dl increase Illumina
[368,274]		 N
04/22/09 Mangino
April 08, 2009
J Med Genet
A genome-wide association study identifies a novel locus on chromosome 18q12.2 influencing white cell telomere length. 		Telomere length 1,625 women 1,165 individuals 18q12.2 BRUNOL4, PIKC3C rs2162440-G NR 3 x 10-6 106 [62.88-149.12] base pairs shorter Illumina
[~314,075]		 N
04/14/09 Esparza-Gordillo
April 06, 2009
Nat Genet
A common variant on chromosome 11q13 is associated with atopic dermatitis. 		Atopic dermatitis 939 cases, 975 controls, 1,097 family members 2,637 cases, 3,957 controls 11q13.5 C11orf30 rs7927894-A 0.36 8 x 10-10 1.22 [1.15-1.30] Affymetrix
[342,303]		 N
04/16/09 Kamatani
April 06, 2009
Nat Genet
A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. 		Hepatitis B 179 Japanese cases, 934 Japanese controls 1,599 Japanese cases, 2,821 Japanese controls, 308 Thai cases, 546 Thai controls 6p21.32 HLA-DPB1 rs9277535-G 6 x 10-39 1.75 [1.61-1.92] Illumina
[499,544]		 N
05/11/09 Yamada
April 05, 2009
Atherosclerosis
Identification of CELSR1 as a susceptibility gene for ischemic stroke in Japanese individuals by a genome-wide association study 		Ischemic stroke 131 cases, 135 controls 776 cases, 5,205 controls NS NS NS NS NS NS Affymetrix
[~520,000]		 N
04/22/09 Soranzo
April 03, 2009
PLoS Genet
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. 		Height 12,611 individuals 7,187 individuals 12q14.3
20q11.22
3q23
6p22.1
7p15.1
6q24.1
6p21.31
13q14.3
7p22.2
4p15.32
7q21.2
4q21.21
15q25.2
6p21.33
1p36.11
14q24.3
5p13.3
9p13.3
4q31.22
8q12.1		 HMGA2
UQCC
ZBTB38
HIST1H1D
JAZF1
GPR126
HMGA1,C6orf106
DLEU7
GNA12
LCORL
CDK6
PRKG2
ADAMTSL3
HLA-B
CATSPER4
TMED10
NPR3
WDR40A
HHIP
PLAG1		 rs8756-?
rs6088813-?
rs6763931-?
rs10946808-?
rs849141-?
rs6570507-?
rs1776897-?
rs3118914-?
rs1182188-?
rs6830062-?
rs2282978-?
rs710841-?
rs4842838-?
rs13437082-?
rs11809207-?
rs910316-?
rs10472828-?
rs7871764-?
rs1812175-?
rs7815788-?		 0.17
0.11
0.35
0.43
0.23
0.42
0.49
0.39
0.27
0.23
0.08
0.12
0.32
0.13
0.23
0.15
0.26
0.44
0.49
0.39		 5 x 10-14
1 x 10-13
3 x 10-12
6 x 10-12
3 x 10-11
4 x 10-11
8 x 10-11
4 x 10-10
3 x 10-9
5 x 10-9
1 x 10-8
2 x 10-8
3 x 10-8
5 x 10-8
6 x 10-8
1 x 10-7
3 x 10-7
2 x 10-6
4 x 10-6
5 x 10-6 		.08 [0.06-0.10] s.d. decrease
.09 [0.07-0.11] s.d. decrease
.07 [0.05-0.09] s.d. increase
.07 [0.04-0.10] s.d. increase
.08 [0.06-0.10] s.d. increase
.08 [0.06-0.10] s.d. decrease
.12 [0.08-0.16] s.d. increase
.08 [0.05-0.11] s.d. decrease
.07 [0.04-0.10] s.d. increase
.1 [0.07-0.13] s.d. increase
.06 [0.04-0.08] s.d. decrease
.07 [0.04-0.10] s.d. increase
.06 [0.04-0.07] s.d. decrease
.07 [0.04-0.10] s.d. decrease
.07 [0.04-0.10] s.d. increase
.05 [0.03-0.07] s.d. increase
.06 [0.04-0.08] s.d. decrease
.06 [0.03-0.09] s.d. increase
.06 [0.03-0.09] s.d. decrease
.07 [0.04-0.10] s.d. decrease		 Illumina
[229,216]		 N
04/13/09 Nan
April 02, 2009
J Invest Dermatol
Genome-wide association study of tanning phenotype in a population of European ancestry. 		Tanning 2,287 women 870 controls 6p25.3
11q14.3
5p13.3
16q24.3
11q14.3
16q24.3
14q32.2
12q13.13
21q22.3
5q33.1		 EXOC2
TYR
MATP
MC1R
GRM5
MC1R
Intergenic
LOC440100
PRDM15
PPARGC1B		 rs12210050-T
rs1393350-A
rs35391-T
rs11648785-T
rs10831496-G
rs154659-C
rs17094273-A
rs7969151-A
rs7279297-G
rs32579-A		 NR
NR
NR
NR
NR
NR
NR
0.21
NR
NR		 5 x 10-14
2 x 10-13
3 x 10-10
3 x 10-9
5 x 10-9
7 x 10-8
9 x 10-8
2 x 10-6
3 x 10-6
4 x 10-6 		.22 [0.16-0.28] increase in tanning ability score
.19 [0.13-0.25] increase in tanning ability score
.44 [0.30-0.58] decrease in tanning ability score
.14 [0.10-0.18] decrease in tanning ability score
.14 [0.10-0.18] decrease in tanning ability score
.14 [0.08-0.20] increase in tanning ability score
.2 [0.12-0.28] increase in tanning ability score
.13 [0.07-0.19] increase in tanning ability score
.12 [0.06-0.18] decrease in tanning ability score
.11 [0.07-0.15] decrease in tanning ability score		 Illumina
[528,173]		 N
12/29/09 Danik
April 01, 2009
Circ Cardiovasc Genet
Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study. 		Fibrinogen 17,686 white women NR 4q32.1
5q31.1
1q21.3
17q25.1
2q34
5q31.1		 FGB, FGA, FGG
SLC22A5, SLC22A4, IRF1
IL6R
CD300LF, SLC9A3R1, NAT9
CPS1
SLC22A5, SLC22A4, IRF1		 rs6056-A
rs1016988-G
rs8192284-C
rs10512597-A
rs7422339-A
rs10479002-C		 0.18
0.20
0.40
0.18
0.31
0.04		 8 x 10-39
1 x 10-12
2 x 10-11
8 x 10-11
9 x 10-9
1 x 10-6 		12.94 [NR] mg/dl increase
6.84 [NR] mg/dl decrease
5.3 [NR] mg/dl decrease
6.45 [NR] mg/dl decrease
4.84 [NR] mg/dl decrease
9.51 [NR] mg/dl increase		 Illumina
[337,343]		 N
12/29/09 Dehghan
April 01, 2009
Circ Cardiovasc Genet
Association of novel genetic Loci with circulating fibrinogen levels: a genome-wide association study in 6 population-based cohorts. 		Fibrinogen 22,096 European descent individuals 17,686 white women 4q31.3
5q31.1
3q22.3
1q44		 FGB
IRF1
PCCB
NLRP3		 rs1800789-A
rs2522056-A
rs511154-A
rs1539019-A		 0.22
0.21
0.22
0.37		 2 x 10-30
1 x 10-15
6 x 10-10
1 x 10-8 		.09 [0.07-0.11] g/L increase
.06 [0.04-0.08] g/L decrease
.05 [0.03-0.06] g/L increase
.04 [0.03-0.05] g/L decrease		 Affymetrix & Illumina
[~2,661,766] (imputed)		 N
12/29/09 Pare
April 01, 2009
Circ Cardiovasc Genet
Novel associations of CPS1, MUT, NOX4, and DPEP1 with plasma homocysteine in a healthy population: a genome-wide evaluation of 13 974 participants in the Women's Genome Health Study. 		Plasma homocysteine 13,974 white females 840 European ancestry females 1p36.22
21q22.3		 MTHFR
CBS		 rs1801133-A
rs6586282-?		 0.33
0.18		 8 x 10-35 (WGHS)
3 x 10-10 (WGHS)		 .05 [NR] unit increase in log(homocysteine)
.03 [NR] unit decrease in log(homocysteine)		 Illumina
[336,469]		 N
12/29/09 Tarasov
April 01, 2009
Circ Cardiovasc Genet
COL4A1 is associated with arterial stiffness by genome-wide association scan. 		Arterial stiffness 4,221 Sardinian individuals 1,828 Sardinian individuals, 813 Old-Order Amish individuals 13q34 COL4A1 rs3742207-C 0.44 5 x 10-8 21 [11.79-30.21] cm/s increase Affymetrix
[362,129] (imputed)		 N
12/29/09 Thompson
April 01, 2009
Circ Cardiovasc Genet
Comprehensive Whole-Genome and Candidate Gene Analysis for Response to Statin Therapy in the Treating to New Targets (TNT) Cohort 		Response to statin therapy 1,984 individuals 5,009 individuals NS NS NS NS NS NS Perlegen
[291,998]		 N
04/03/09 Thomas
March 29, 2009
Nat Genet
A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). 		Breast cancer 1,145 cases, 1,142 controls 8,625 cases, 9,657 controls 10q26.13
1p11.2
16q12.1
2q35
14q24.1
5q11.2		 FGFR2
Intergenic
TOX3
Intergenic
RAD51L1
MAP3K1		 rs2981579-T
rs11249433-C
rs3803662-T
rs13387042-A
rs999737-C
rs16886165-G		 0.41
0.39
0.27
0.51
0.76
0.15		 2 x 10-10
7 x 10-10
1 x 10-9
2 x 10-8
2 x 10-7
5 x 10-7 		1.17 [1.07-1.27]
1.16 [1.09-1.24]
1.16 [1.07-1.27]
1.25 [1.15-1.37]
1.06 [1.01-1.14]
1.23 [1.12-1.35]		 Illumina
[528,173]		 N
03/31/09 Newton-Cheh
March 22, 2009
Nat Genet
Common variants at ten loci influence QT interval duration in the QTGEN Study. 		QT interval 13,685 individuals 15,854 individuals 1q23.3
1q23.3
1q23.3
16q21
6q22.31
11p15.5
1p36.31
7q36.1
7q36.1
11p15.5
16p13.13
3p22.2
17q12		 NOS1AP
NOS1AP
NOS1AP
CNOT1,GINS3, NDRG4, SLC38A7, GOT2
c6orf204,SLC35F1, PLN, ASF1A
KCNQ1
RNF207,NPHP4, CHDS, ACOT7, PLEKHG5, KLH21
KCNH2
KCNH2
KCNQ1
LITAF,CLEC16A, SNN, ZC3H7A, TNFRSF17
SCN5A
LIG3,RFFL		 rs12143842-T
rs12029454-A
rs16857031-G
rs37062-G
rs11756438-A
rs2074238-T
rs846111-C
rs4725982-T
rs2968864-C
rs12576239-T
rs8049607-T
rs12053903-C
rs2074518-T		 0.26
0.15
0.14
0.24
0.47
0.06
0.28
0.22
0.25
0.13
0.49
0.34
0.46		 2 x 10-78
3 x 10-45
1 x 10-34
3 x 10-25
5 x 10-22
3 x 10-17
1 x 10-16
5 x 10-16
8 x 10-16
1 x 10-15
5 x 10-15
1 x 10-14
6 x 10-12 		3.15 [2.81-3.49] msec increase
2.98 [2.63-3.32] msec increase
2.63 [2.28-2.97] msec increase
1.75 [1.41-2.09] msec decrease
1.4 [1.06-1.74] msec increase
7.88 [6.16-9.59] msec decrease
1.75 [1.41-2.09] msec increase
1.58 [1.23-1.92] msec increase
1.4 [1.06-1.74] msec decrease
1.75 [1.41-2.09] msec increase
1.23 [0.88-1.57] msec increase
1.23 [0.88-1.57] msec decrease
1.05 [0.71-1.39] msec decrease		 Affymetrix and Illumina
[up to 2,543,686] (imputed)		 N
04/02/09 Pfeufer
March 22, 2009
Nat Genet
Common variants at ten loci modulate the QT interval duration in the QTSCD Study. 		QT interval 15,842 individuals up to 13,602 individuals 1q23.3
1q23.3
16q21
6q22.31
6q22.31
11p15.5
1p36.31
1q24.2
7q36.1
16p13.13
3p22.2
17q24.3		 NOS1AP
NOS1AP
NDRG4
PLN
PLN
KCNQ1
RNF207
ATP1B1
KCNH2
LITAF
SCN5A
KCNJ2		 rs12143842-T
rs4657178-T
rs7188697-A
rs11970286-T
rs12210810-C
rs12296050-T
rs846111-C
rs10919071-A
rs2968863-T
rs8049607-T
rs11129795-A
rs17779747-T		 0.24
0.33
0.74
0.44
0.06
0.20
0.29
0.87
0.29
0.46
0.23
0.35		 2 x 10-78
7 x 10-33
7 x 10-25
2 x 10-24
2 x 10-17
3 x 10-17
4 x 10-16
1 x 10-15
2 x 10-15
6 x 10-15
5 x 10-14
6 x 10-12 		2.88 [2.43-3.33] ms increase
2.19 [1.76-2.62] ms increase
1.66 [1.20-2.12] ms increase
1.64 [1.25-2.03] ms increase
3.13 [2.29-3.97] ms decrease
1.44 [0.95-1.93] ms increase
1.49 [1.00-1.98] ms increase
2.05 [1.48-2.62] ms increase
1.35 [0.90-1.80] ms decrease
1.25 [0.81-1.69] ms increase
1.27 [0.82-1.72] ms decrease
1.02 [0.53-1.51] ms decrease		 Affymetrix and Illumina
[unsure] (imputed)		 N
04/02/09 Org
March 20, 2009
Hum Mol Genet
Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations. 		Hypertension 364 cases, 590 controls 1,043 cases, 1,769 controls 16q23.3 CDH13 rs11646213-T 0.60 8 x 10-6 1.28 [1.15-1.43] Affymetrix
[395,912]		 N
03/31/09 Pillai
March 20, 2009
PLoS Genet
A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. 		Chronic obstructive pulmonary disease 823 cases, 810 controls 2,840 family members, 389 cases, 472 controls 15q25.1
4q31.22		 CHRNA3,CHRNA4,CHRNA5, IREB2, PSMA4, Q9UD29
HHIP		 rs8034191-C
rs1828591-?		 0.33
NR		 1 x 10-10
1 x 10-7 		1.4 [1.18-1.67]
1.38 [1.17-1.63]		 Illumina
[493,609]		 N
03/30/09 Takeuchi
March 20, 2009
PLoS Genet
A genome-wide association study confirms VKORC1, CYP2C9, and CYP4F2 as principal genetic determinants of warfarin dose. 		Warfarin maintenance dose 1,053 individuals 588 individuals 16p11.2
10q23.33
10q23.33
19p13.12		 VKORC1
CYP2C9
CYP2C9
CYP4F2		 rs9923231-T
rs1057910-?
rs1799853-?
rs2108622-?		 0.40
0.07
0.11
0.24		 3 x 10-181
3 x 10-79
1 x 10-31
3 x 10-10 		.97 [0.91-1.02] mg/week decrease
1.11 [1.00-1.22] mg/week decrease
.54 [0.45-0.63] mg/week decrease
.21 [0.14-0.27] mg/week increase		 Illumina
[325,997]		 N
03/31/09 Wilk
March 20, 2009
PLoS Genet
A genome-wide association study of pulmonary function measures in the Framingham Heart Study. 		Pulmonary function measures 7,691 individuals 835 individuals 4q31.22 HHIP rs13147758-G 0.39 8 x 10-11 .1 [NR] % increase in FEV1/FVC ratio Affymetrix
[2,540,223] (imputed)		 N
04/01/09 Tanaka
March 18, 2009
Am J Hum Genet
Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations. 		Folate pathway vitamin levels 2,934 individuals 686 individuals 19q13.33
1p36.12
10p13
11q12.1
3p14.1		 FUT2
ALPL
CUBN
TCN1
PRICKLE2		 rs602662-A
rs4654748-C
rs11254363-A
rs526934-A
rs153734-T		 0.53
0.50
0.70
0.67
0.84		 3 x 10-20 (vitamin B12)
8 x 10-18 (vitamin B6)
1 x 10-6 (vitamin B12)
2 x 10-6 (vitamin B12)
7 x 10-6 (folate)		 49.77 [37.09-62.45] pg/ml increase
1.45 [0.90-2.00] ng/ml decrease
21.49 [7.71-35.27] pg/mL decrease
27.62 [11.65-43.59] pg/mL increase
.29 [0.13-0.45] ng/ml increase		 Affymetrix and Illumina
[~2.5 million] (imputed)		 N
03/31/09 Kilpivaara
March 15, 2009
Nat Genet
A germline JAK2 SNP is associated with predisposition to the development of JAK2(V617F)-positive myeloproliferative neoplasms. 		Myeloproliferative neoplasms 324 cases, 2,999 controls NR 9p24.1 JAK2 rs10974944-? NR 4 x 10-20 3.1 [2.40-4.00] Affymetrix
[62,775]		 N
03/31/09 Cui
March 14, 2009
Mol Med
Genome-wide association study of determinants of anti-cyclic citrullinated peptide antibody titer in adults with rheumatoid arthritis. 		Anti-cyclic Citrullinated Peptide Antibody 531 individuals with rheumatoid arthritis 849 individuals with rheumatoid arthritis 6p21.32 HLA-DRA, BTNL2 rs1980493-? 0.13 5 x 10-7 NR Affymetrix
[97,248]		 N
03/29/09 Liu
March 13, 2009
PLoS Genet
Genome-wide association analyses identify SPOCK as a key novel gene underlying age at menarche 		Menarche (age at onset) 477 women 854 siblings, 762 women, 1,387 Chinese women NS NS NS NS NS NS Affymetrix
[379,319]		 N
03/30/09 Tregouet
March 10, 2009
Blood
Common susceptibility alleles are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. 		Venous thromboembolism 419 cases, 1,228 controls 1,757 cases, 1,480 controls 9q34.2 ABO rs505922-C 0.35 4 x 10-15 1.81 [1.56-2.11] Illumina
[291,872]		 N
03/28/09 Birnbaum
March 08, 2009
Nat Genet
Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. 		Nonsyndromic cleft lip with or without cleft palate 224 cases, 383 controls 246 cases, 954 controls 8q24.21
1q32.2		 PVT1, GSDMC
IRF6		 rs987525-A
rs642961-A		 0.20
NR		 3 x 10-24
2 x 10-6 		2.57 [2.02-3.26]
NR		 Illumina
[521,176]		 N
03/24/09 Liu
March 04, 2009
Am J Hum Genet
Genome-wide association and replication studies identified TRHR as an important gene for lean body mass. 		Body mass (lean) 1,000 individuals 1,488 individuals, 1,972 family members, 2,955 Chinese individuals 8q23.1 TRHR rs7832552-T 0.32 4 x 10-10 .1 [0.04-0.16] kg increase Affymetrix
[379,319]		 N
03/24/09 Vink
March 04, 2009
Am J Hum Genet
Genome-wide Association Study of Smoking Initiation and Current Smoking 		Smoking behavior 3,540 individuals 6,405 individuals, 824 twin pairs NS NS NS NS NS NS Perlegen
[427,037]		 N
03/28/09 Hattori
March 02, 2009
Am J Med Genet B Neuropsychiatr Genet
Preliminary genome-wide association study of bipolar disorder in the Japanese population 		Bipolar disorder 107 cases, 107 controls 395 cases, 409 controls NS NS NS NS NS NS Affymetrix
[88,671]		 N
04/01/09 Caporaso
February 27, 2009
PLoS One
Genome-wide and candidate gene association study of cigarette smoking behaviors. 		Smoking behavior 4,611 individuals (2,617 smokers) NR 3q13.12
1p22.3
1p35.2
3q24
12q21.2
16p13.2
18q11.2
19p12
5q14.3
9p21.2
9q31.1
Xq23
14q24.1
17p13.2
Xp11.3
12q21.33
13q33.1
4q31.1
7p15.2
3q27.2
4q28.1		 BBX
AK002179
Intergenic
Intergenic
Intergenic
Intergenic
CABLES1
ZNF505
LOC133789
Intergenic
Intergenic
TRPC5
ACTN1
CAMKK1
MAOA
Intergenic
Intergenic
SET7
Intergenic
Intergenic
Intergenic		 rs6437740-?
rs7553864-?
rs910696-?
rs800082-?
rs1402279-?
rs3112740-?
rs11082304-?
rs10411195-?
rs933688-?
rs1889899-?
rs10989661-?
rs7050529-?
rs2268983-?
rs758642-?
rs3027409-?
rs1847461-?
rs912969-?
rs17050782-?
rs886716-?
rs6444087-?
rs950063-?		 0.24
0.39
0.31
0.42
0.95
0.86
0.49
0.03
0.17
0.37
0.74
0.07
0.51
0.34
0.95
0.94
0.07
0.21
0.69
0.26
0.39		 2 x 10-7 (CPD)
3 x 10-6 (SMKDU)
3 x 10-6 (CPD)
3 x 10-6 (PKYRS)
5 x 10-6 (EVNV)
6 x 10-6 (CPDBI)
6 x 10-6 (SMKAGE)
6 x 10-6 (CPD)
6 x 10-6 (EVNV)
6 x 10-6 (EVNV)
6 x 10-6 (CIGSTAT)
6 x 10-6 (CPD)
7 x 10-6 (CPDBI)
7 x 10-6 (CPD)
7 x 10-6 (CPDBI)
8 x 10-6 (CIGSTAT)
8 x 10-6 (SMKDU)
8 x 10-6 (SMKAGE)
8 x 10-6 (CPDBI)
9 x 10-6 (EVNV)
9 x 10-6 (SMKDU)		 .1 [NR] fewer cigarettes per day
.08 [NR] more years
.08 [NR] more cigarettes per day
.12 [NR] more pack years
1.51 [NR]
2.16 [NR]
.03 [NR] years older
.21 [NR] fewer cigarettes per day
1.48 [NR]
1.26 [NR]
1.68 [NR]
.06 [NR] fewer cigarettes per day
1.52 [NR]
.08 [NR] more cigarettes per day
1.73 [NR]
1.8 [NR]
.14 [NR] fewer years
.03 [NR] years older
1.52 [NR]
1.28 [NR]
.08 [NR] fewer years		 Illumina
[~518,000]		 N
03/18/09 Pezzolesi
February 27, 2009
Diabetes
Genome-wide Association Scan for Diabetic Nephropathy Susceptibility Genes in Type 1 Diabetes Mellitus 		Diabetic nephropathy 820 cases, 885 controls 1,304 individuals NS NS NS NS NS NS Affymetrix
[359,193]		 N
03/18/09 Gu
February 25, 2009
Nature
Identification of IFRD1 as a modifier gene for cystic fibrosis lung disease 		Cystic fibrosis severity 160 severe lung disease patients, 160 mild lung disease patients (all homozygous for CFTR deltaF508 variant) 101 severe lung disease patients, 381 mild lung disease patients, 1,118 family members NS NS NS NS NS NS Affymetrix
[100,198] (pooled)		 N
03/18/09 Xiong
February 25, 2009
Am J Hum Genet
Genome-wide association and follow-up replication studies identified ADAMTS18 and TGFBR3 as bone mass candidate genes in different ethnic groups. 		Bone mineral density 1,000 white individuals 4,925 white individuals, 350 Chinese hip fracture cases, 350 Chinese controls, 2,955 Chinese individuals, 908 West African men 16q23.1
1p22.2		 ADAMTS18
TGFBR3		 rs11864477-C
rs17131547-A		 0.12
0.01		 2 x 10-8 (hip BMD)
1 x 10-6 (spine BMD)		 1 % [NR] of variance explained
1.2 % [NR] of variance explained		 Affymetrix
[379,319]		 N
03/01/09 Schrauwen
February 18, 2009
Am J Hum Genet
A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis. 		Otosclerosis 302 cases, 302 controls 847 cases, 872 controls 7q22.1 RELN rs3914132-? 0.23 2 x 10-8 1.54 [1.32-1.79] Illumina
[~555,000] (pooled)		 N
05/07/09 Smith
February 15, 2009
Heart Rhythm
Genome-wide association study of electrocardiographic conduction measures in an isolated founder population: Kosrae. 		Electrocardiographic conduction measures 1,262 Kosraen individuals NR 3p22.2
4p16.1
3p22.2
1q32.1
4q31.3
2q31.1
6p12.2		 SCN5A
MSX1
SCN5A
NR
NR
Intergenic
NR		 rs7638909-G
rs2008242-?
rs2070488-A
rs7512898-?
rs17030434-?
rs2461751-G
rs283566-?		 0.40
0.15
0.33
0.41
0.43
0.44
0.16		 2 x 10-6 (PR interval)
3 x 10-6 (PR segment)
4 x 10-6 (PR interval)
5 x 10-6 (PR segment)
5 x 10-6 (P wave duration)
8 x 10-6 (PR interval)
9 x 10-6 (P wave duration)		 4.8 [2.84-6.76] ms increase
NR
5 [2.84-7.16] ms decrease
NR
NR
4.54 [2.58-6.50] ms increase
NR		 Affymetrix
[338,049]		 N
02/28/09 Zheng
February 15, 2009
Nat Genet
Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. 		Breast cancer 1,505 Chinese cases, 1,522 Chinese controls 1,554 Chinese cases, 1,576 Chinese controls 6q25.1 C6orf97 rs2046210-A 0.37 2 x 10-15 1.29 [1.21-1.37] Affymetrix
[up to 607,728]		 N
02/28/09 Soranzo
February 12, 2009
Blood
A novel variant on chromosome 7q22.3 associated with mean platelet volume, counts, and function. 		Mean platelet volume 1,221 individuals 7,365 individuals 7q22.3 Intergenic rs342293-G 0.45 1 x 10-24 .02 [0.014-0.018] log fl increase Affymetrix
[361,352]		 N
03/01/09 Erdmann
February 08, 2009
Nat Genet
New susceptibility locus for coronary artery disease on chromosome 3q22.3. 		Coronary artery disease 6,990 cases, 8,955 controls 12,417 cases, 12,411 controls 3q22.3
12q24.31		 MRAS
HNF1A,C12orf43		 rs9818870-T
rs2259816-T		 0.15
0.36		 7 x 10-13
5 x 10-7 		1.15 [1.11-1.19]
1.08 [1.05-1.11]		 Affymetrix
[567,119]		 N
03/01/09 Gudbjartsson
February 08, 2009
Nat Genet
Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. 		Plasma eosinophil count 9,392 individuals 12,118 individuals 12q24.12
3q21.3
2q12.1
5q31.1
2q34
5q22.1
6p21.32		 SH2B3
GATA2
IL1RL1
IL5
IKZF2
WDR36, TSLP
MHC		 rs3184504-T
rs4857855-T
rs1420101-A
rs4143832-C
rs12619285-G
rs2416257-G
rs2269426-T		 0.38
0.82
0.41
0.16
0.74
0.85
0.76		 7 x 10-19 (European)
9 x 10-17 (European)
5 x 10-14 (European)
1 x 10-10 (European)
5 x 10-10 (European)
1 x 10-6 (European)
3 x 10-6 (European)		 7.6 [5.9-9.3] % standard unit increase
9.4 [7.2-11.6] % standard unit increase
6.4 [4.7-8.1] % standard unit increase
7.1 [4.9-9.2] % standard unit increase
6.3 [4.3-8.3] % standard unit increase
6.1 [3.7-8.6] % standard unit increase
4.6 [2.7-6.6] % standard unit increase		 Illumina
[312,179]		 N
03/01/09 Kathiresan
February 08, 2009
Nat Genet
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variants. 		Myocardial infarction (early onset) 2,967 cases, 3,075 controls 9,746 cases, 9,746 controls 9p21.3
1p13.3
21q22.11
1q41
6p24.1
19p13.2
10q11.21
1p32.3
2q33.1		 CDKN2A, CDKN2B
CELSR2, PSRC1, SORT1
SLC5A3, MRPS6, KCNE2
MIA3
PHACTR1
LDLR
CXCL12
PCSK9
WDR12		 rs4977574-G
rs646776-T
rs9982601-T
rs17465637-C
rs12526453-C
rs1122608-G
rs1746048-C
rs11206510-T
rs6725887-C		 0.56
0.81
0.13
0.72
0.65
0.75
0.84
0.81
0.14		 3 x 10-44
8 x 10-12
6 x 10-11
1 x 10-9
1 x 10-9
2 x 10-9
7 x 10-9
1 x 10-8
1 x 10-8 		1.29 [1.25-1.34]
1.19 [1.13-1.26]
1.2 [1.14-1.27]
1.14 [1.10-1.19]
1.12 [1.08-1.17]
1.15 [1.10-1.20]
1.17 [1.11-1.24]
1.15 [1.10-1.21]
1.17 [1.11-1.23]		 Affymetrix
[~2.5 million] (imputed)		 N
04/01/09 Tregouet
February 08, 2009
Nat Genet
Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease 		Coronary artery disease 1,926 cases, 2,938 controls 7,073 cases, 7,325 controls 6q25.3
6q25.3		 SLC22A3,LPAL2,LPA
SLC22A3,LPAL2,LPA		 4-SNP haplotype-2
4-SNP haplotype-1		 0.02
0.16		 4 x 10-15 (CCTC)
1 x 10-9 (CTTG)		 1.82 [1.57-2.12]
1.2 [1.13-1.28]		 Affymetrix
[~500,000]		 N
02/28/09 Gudmundsson
February 06, 2009
Nat Genet
Common variants on 9q22.33 and 14q13.3 predispose to thyroid cancer in European populations. 		Thyroid cancer 192 cases, 37,196 controls 432 cases, 1,727 controls 9q22.33
14q13.3		 FOXE1
NKX2-1		 rs965513-A
rs944289-T		 0.34
0.57		 2 x 10-27
2 x 10-9 		1.75 [1.59-1.94]
1.37 [1.24-1.52]		 Illumina
[304,083]		 N
10/15/09 Lowe
February 06, 2009
PLoS Genet
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. 		Quantitative traits Up to 2,906 Micronesian individuals NR 11q23.3
19q13.32
19q13.32
3q25.33
10p12.33
5q13.3
7p22.2
9q22.33
10p15.3
12p13.33
19q13.32
19q13.32
20q13.12
7p14.1
7q36.3
9p21.3
2q22.2
12q24.13
12q24.31
19q13.32
5q35.3
9p21.3
10p13
10p13
2p23.3
5q13.3
5q35.1
4q21.21
10p15.3
6q16.2
6p22.3
7p21.3
7q34		 Intergenic
TOMM40, APOC2, APOE, APOC4, APOC1
MGC2650, BLOC1S3, XTP7
SCHIP1
CACNB2
COL4A3BP, HMGCR
SDK1
HEMGN, C9ORF156
ADARB2
ENSG00000118975, FKBP4
MGC2650, BLOC1S3, XTP7
TOMM40, APOC2, APOE, APOC4, APOC1
Intergenic
Intergenic
UBE3C
Intergenic
ARHGAP15
Intergenic
SPPL3
TOMM40, APOC2, APOE, APOC4, APOC1
MGAT1
Intergenic
ITGA8
CUBN
ENSG00000173957, UBXD4, FKBP1B, FLJ21945
COL4A3BP, HMGCR
Intergenic
Intergenic
ADARB2
Intergenic
Intergenic
Intergenic
TRIM24		 rs7396835-T
rs4420638-G
rs2159324-T
rs2222328-C
rs7069923-C
rs3846663-T
rs6462411-C
rs755109-C
rs6560749-T
rs10848704-C
rs2159324-T
rs4420638-G
rs6066084-A
rs10486715-A
rs2527866-C
rs2225614-C
rs10928195-C
rs11066587-G
rs1039302-T
rs4420638-G
rs655601-A
rs613391-G
rs7895372-G
rs10508517-A
rs7561273-A
rs3846663-T
rs254893-A
rs10518224-A
rs6560749-T
rs6909430-G
rs10498712-G
rs17157663-A
rs1874326-G		 0.32
0.21
0.44
0.32
0.49
0.39
0.20
0.23
0.14
0.35
0.44
0.21
0.06
0.07
0.23
0.50
0.08
0.16
0.36
0.21
0.47
0.49
0.04
0.43
0.35
0.39
0.06
0.23
0.14
0.08
0.25
0.32
0.47		 1 x 10-9 (TG)
3 x 10-7 (TC)
4 x 10-7 (LDL-C)
8 x 10-7 (WC)
1 x 10-6 (SBP)
1 x 10-6 (LDL-C)
1 x 10-6 (TSH)
1 x 10-6 (TSH)
2 x 10-6 (BMI)
2 x 10-6 (TSH)
2 x 10-6 (CRP)
2 x 10-6 (CRP)
2 x 10-6 (% body fat)
3 x 10-6 (height)
3 x 10-6 (SBP)
3 x 10-6 (weight)
4 x 10-6 (weight)
5 x 10-6 (CRP)
5 x 10-6 (CRP)
5 x 10-6 (TG)
5 x 10-6 (HDL-C)
5 x 10-6 (WC)
6 x 10-6 (TC)
6 x 10-6 (DBP)
6 x 10-6 (CRP)
6 x 10-6 (TC)
6 x 10-6 (DBP)
7 x 10-6 (TG)
8 x 10-6 (% body fat)
8 x 10-6 (TSH)
9 x 10-6 (HDL-C)
9 x 10-6 (TC)
9 x 10-6 (weight)		 .23 [NR] mg/dL increase
.28 [NR] mg/dL increase
.21 [NR] mg/dL decrease
.22 [NR] inch decrease
.19 [NR] mm Hg increase
.21 [NR] mg/dL increase
.36 [NR] mIU/L decrease
.31 [NR] mIU/L decrease
.32 [NR] kg/m2 decrease
.29 [NR] mIU/L decrease
.19 [NR] mg/L decrease
.28 [NR] mg/L decrease
.85 [NR] % increase
.44 [NR] inch decrease
.27 [NR] mm Hg decrease
.21 [NR] lb. decrease
.36 [NR] lb. decrease
.26 [NR] mg/L increase
.21 [NR] mg/L increase
.22 [NR] mg/dL increase
.23 [NR] mg/dL increase
.2 [NR] inch increase
.35 [NR] mg/dL decrease
.18 [NR] mm Hg decrease
.22 [NR] mg/L decrease]
.19 [NR] mg/dL increase
.58 [NR] mm Hg decrease
.19 [NR] mg/dL increase
.34 [NR] % decrease
.49 [NR] mIU/L decrease
.23 [NR] mg/dL increase
.18 [NR] mg/dL decrease
.22 [NR] lb. increase		 Affymetrix
[408,775]		 N
08/21/09 Need
February 06, 2009
PLoS Genet
A genome-wide investigation of SNPs and CNVs in schizophrenia 		Schizophrenia 871 European ancestry cases, 863 European ancestry controls 1,460 European ancestry cases, 12,995 European ancestry controls NS NS NS NS NS NS Illumina
[312,565]		 N
02/27/09 Garcia-Barcelo
February 05, 2009
Proc Natl Acad Sci U S A
Genome-wide association study identifies NRG1 as a susceptibility locus for Hirschsprung's disease. 		Hirschsprung's disease 181 Chinese cases, 346 Chinese controls 190 Chinese cases, 510 Chinese controls 10q11.21
8p12		 RET, GALNACT-2, RASGEF1A
NRG1		 rs2742234-T
rs16879552-G		 NR
0.61		 4 x 10-18
2 x 10-8 		NR
1.68 [1.40-2.00]		 Affymetrix
[293,836]		 N
03/31/09 Chio
February 04, 2009
Hum Mol Genet
A two-stage genome-wide association study of sporadic amyotrophic lateral sclerosis 		Amyotrophic lateral sclerosis 553 cases, 2,338 controls 3,149 cases, 3,335 controls NS NS NS NS NS NS Illumina
[545,066]		 N
02/27/09 Liu
February 03, 2009
Mol Psychiatry
Genome-wide association analyses suggested a novel mechanism for smoking behavior regulated by IL15 		Smoking behavior 417 Caucasian males, 423 Caucasian females 412 African American males, 839 African American females, 3,491 Caucasian males, 4,132 Caucasian females NS NS NS NS NS NS Affymetrix
[379,319]		 N
02/28/09 Kim
February 01, 2009
Clin Exp Allergy
Alpha-T-catenin (CTNNA3) gene was identified as a risk variant for toluene diisocyanate-induced asthma by genome-wide association analysis. 		Asthma (toluene diisocyanate-induced) 84 Korean cases, 263 Korean controls NR 13q12.13
10q21.3
9p21.3		 Intergenic
CTNNA3
Intergenic		 rs9319321-T
rs10762058-G
rs16937883-G		 0.29
0.25
0.02		 3 x 10-6
6 x 10-6
7 x 10-6 		5.2 [2.47-10.92]
5 [2.36-10.6]
5.29 [2.41-11.61]		 Affymetrix
[312,978]		 N
02/27/09 Kim
February 01, 2009
Pharmacogenomics
Genome-wide association study of acute post-surgical pain in humans. 		Pain 60 females, 52 males NR 19p12
11q23.3
1p21.3		 LOC400680, ZNF429
NR
NR		 rs2562456-?
rs17122021-?
rs6693882-?		 NR
NR
NR		 2 x 10-10 (onset time of analgesia)
7 x 10-7 (maximum post-operative pain rating)
2 x 10-6 (post-operative pain onset time)		 NR
NR
NR		 Affymetrix
[374,975]		 N
03/30/09 Polasek
February 01, 2009
Croat Med J
Genome-wide association study of anthropometric traits in Korcula Island, Croatia. 		Anthropometric traits 898 individuals NR 16p11.2
14q32.13
14q23.3
5q33.3
7q22.1
1p36.32
7q22.1
13q14.3
2q31.1
5q33.3
7q22.1
2p22.3
5q33.2		 SEZ6L2
LOC122509, FAM14B
MAX
SGCD
ZNF498
Intergenic
ZNF498
ZNF498
Intergenic
SGCD
ZNF498
CRIM1
AMPA 1, GRIA1		 rs4787483-?
rs7157940-?
rs7158173-?
rs157350-?
rs7792939-?
rs7513590-?
rs7792939-?
rs7792939-?
rs7590983-?
rs157350-?
rs7792939-?
rs1863080-?
rs12658202-?		 0.34
0.46
0.48
0.11
0.15
0.10
0.15
0.28
0.05
0.11
0.15
0.10
0.45		 2 x 10-6 (waist cirumference)
3 x 10-6 (weight)
4 x 10-6 (waist circumference)
4 x 10-6 (brachial circumference)
4 x 10-6 (weight)
5 x 10-6 (height)
5 x 10-6 (brachial circumference)
6 x 10-6 (brachial circumference)
6 x 10-6 (BMI)
6 x 10-6 (hip circumference)
6 x 10-6 (hip circumference)
8 x 10-6 (brachial circumference)
9 x 10-6 (height)		 .16 [0.09-0.23] mm increase
.12 [0.07-0.17] kg increase
.11 [0.06-0.16] mm decrease
.31 [0.18-0.44] mm decrease
.26 [0.15-0.37] kg increase
.31 [0.17-0.45] mm decrease
.26 [0.15-0.37] mm increase
.17 [0.10-0.24] mm increase
.46 [0.26-0.66] kg/m2 increase
.31 [0.18-0.44] mm decrease
.26 [0.15-0.37] mm increase
.31 [0.17-0.45] mm increase
.11 [0.06-0.16] mm increase		 Illumina
[316,730]		 N
12/29/09 Ridker
February 01, 2009
Circ Cardiovasc Genet
Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study. 		HDL cholesterol 18,425 European ancestry females NR 16q13 CETP, NUP93, SLC12A3, HERPUD1 rs1800775-A 0.49 4 x 10-93 3.09 mg/dL increase Illumina
[~318,237]		 N
02/25/09 Stefansson
February 01, 2009
Nat Genet
Variant in the sequence of the LINGO1 gene confers risk of essential tremor. 		Essential tremor 452 cases, 14,378 controls 300 cases, 1,419 controls 15q24.3 LINGO1 rs9652490-G 0.23 1 x 10-9 1.55 [1.35-1.79] Illumina
[305,624]		 N
03/31/09 Zemunik
February 01, 2009
Croat Med J
Genome-wide association study of biochemical traits in Korcula Island, Croatia. 		Biochemical measures 898 individuals NR 4p16.1
12q24.23
4q12
4q13.1
6q16.3
12q12
4q31.23
Xp22.31
12q21.33
12q24.23
4q23
18q12.3
Xq23
20p12.1
21q22.3
21q22.3
16q13		 SLC2A9
KSR2
USP46
LPHN3
GRIK2
Intergenic
NR3C2
Neuroligin 4
Intergenic
KSR2
RAP1GDS1
SLC14A2
ZCCHC16
PCSK2
PKNOX1
PKNOX1
CETP		 rs13129697-C
rs4767631-A
rs346923-A
rs4599440-A
rs12207601-G
rs871392-A
rs1490453-A
rs7885458-G
rs10777332-A
rs10444502-C
rs10516430-A
rs10502868-G
rs5982533-G
rs6044777-A
rs2839619-G
rs2839619-G
rs7499892-A		 0.25
0.31
0.13
0.23
0.16
0.15
0.17
0.24
0.11
0.28
0.28
0.08
0.22
0.17
0.40
0.40
0.16		 1 x 10-9 (uric acid)
6 x 10-7 (LDL cholesterol)
2 x 10-6 (triglycerides)
2 x 10-6 (HDL cholesterol)
2 x 10-6 (fibrinogen)
3 x 10-6 (HDL cholesterol)
3 x 10-6 (fibrinogen)
3 x 10-6 (fibrinogen)
5 x 10-6 (total cholesterol)
6 x 10-6 (total cholesterol)
6 x 10-6 (triglycerides)
7 x 10-6 (albumin)
7 x 10-6 (triglycerides)
8 x 10-6 (fibrinogen)
8 x 10-6 (total cholesterol)
8 x 10-6 (LDL cholesterol)
9 x 10-6 (HDL cholesterol)		 .29 [0.21-0.37] umol/l decrease
.12 [0.11-0.23] mmol/L decrease
.28 [0.17-0.39] mmol/L decrease
.2 [0.12-0.28] mmol/L increase
.26 [0.15-0.37] g/L decrease
.26 [0.15-0.37] mmol/L decrease
.25 [0.15-0.35] g/L increase
.23 [0.13-0.33] g/L decrease
.24 [0.14-0.34] mmol/L decrease
.17 [0.10-0.24] mmol/L decrease
.16 [0.09-0.23] mmol/L decrease
.04 [0.21-0.51] g/L decrease
.23 [0.13-0.33] mmol/L decrease
.23 [0.13-0.33] g/L increase
.13 [0.07-0.19] mmol/L increase
.13 [0.08-0.18] mmol/L increase
.24 [0.14-0.34] mmol/L decrease		 Illumina
[316,730]		 N
02/25/09 Timpson
January 30, 2009
Hum Mol Genet
Common variants in the region around Osterix are associated with bone mineral density and growth in childhood 		Bone mineral density 1,418 children, 135 adults 3,875 children NS NS NS NS NS NS Illumina
[up to 315,807]		 N
02/28/09 Ferrucci
January 29, 2009
Am J Hum Genet
Common variation in the beta-carotene 15,15'-monooxygenase 1 gene affects circulating levels of carotenoids: a genome-wide association study. 		Plasma carotenoid and tocopherol levels 1,191 individuals 2,751 individuals 16q23.2
11q23.3		 BCMO1
APOA5		 rs6564851-G
rs12272004-A		 0.39
0.07		 2 x 10-24 (beta-carotene)
8 x 10-10 (alpha-tocopherol)		 .15 [0.120-0.177] umol/L increase
.07 [0.049-0.095] umol/L increase		 Illumina
[~500,451]		 N
02/26/09 Yang
January 28, 2009
JAMA
Genome-wide interrogation of germline genetic variation associated with treatment response in childhood acute lymphoblastic leukemia. 		Response to treatment for acute lymphoblastic leukemia 487 children NR 10p12.33
2q33.1
4q31.21
20q13.12
7p14.2
7p21.2
10q26.12
11p15.1
6q25.3
5p13.2
10p14
11q21		 ST8SIA6
C2orf47
IL15
NCOA3
ELMO1
DGKB
intergenic
intergenic
intergenic
LMBRD2
Intergenic
MAML2		 rs359312-T
rs1569175-T
rs17007695-C
rs6125048-T
rs4723619-C
rs6971925-T
rs2901286-A
rs7128311-C
rs35229355-T
rs267759-A
rs10508343-A
rs7115578-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 9 x 10-8
9 x 10-7
9 x 10-7
2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6 		3.91 [1.52-10.10]
2.73 [1.52-4.93]
2.67 [1.53-4.68]
2.73 [1.08-6.88]
3.01 [1.50-6.03]
13.91 [2.72-70.92]
4.66 [1.58-13.7]
13.9 [2.72-71.1]
7.24 [2.46-21.30]
3.23 [1.52-6.87]
3.81 [1.40-10.40]
1.86 [1.23-2.79]		 Affymetrix
[476,796]		 N
02/06/09 Nair
January 25, 2009
Nat Genet
Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. 		Psoriasis 1,359 cases, 1,400 controls 5,048 cases, 5,041 controls 6p21.33
5q33.3
5q33.1
5q31.1
6q23.3
12q13.2
1p31.3
9q34.13		 HLA-C
IL12B
TNIP1
IL13
TNFAIP3
IL23A, STAT2
IL23R
TSC1		 rs12191877-T
rs2082412-G
rs17728338-A
rs20541-G
rs610604-G
rs2066808-A
rs2201841-G
rs1076160-T		 0.15
0.80
0.054
0.79
0.32
0.93
0.30
0.48		 1 x 10-100
2 x 10-28
1 x 10-20
5 x 10-15
9 x 10-12
1 x 10-9
3 x 10-8
6 x 10-6 		2.64 [NR]
1.44 [NR]
1.59 [NR]
1.27 [NR]
1.19 [NR]
1.34 [NR]
1.13 [NR]
1.09 [NR]		 Perlegen
[~2.5 million] (imputed)		 N
02/07/09 Zhang
January 25, 2009
Nat Genet
Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. 		Psoriasis 1,139 Chinese cases, 1,132 Chinese controls 5,721 Chinese cases, 7,340 Chinese controls 1q21.3
5q33.3
6p21.33		 LCE3D, LCE3A
IL12B
MHC		 rs4085613-A
rs3213094-A
rs1265181-?		 0.43
0.45
NR		 7 x 10-30
3 x 10-26
x 10 		1.32 [1.25-1.39]
1.28 [1.23-1.35]
22.62 		Illumina
[494,902]		 N
02/26/09 Otowa
January 23, 2009
J Hum Genet
Genome-wide association study of panic disorder in the Japanese population. 		Panic disorder 200 Japanese cases, 200 Japanese controls NR 12p13.31
1q32.1
17q25.1
12q13.13
13q32.1
6q25.1
8p21.1
1p13.3
3p26.1
12q12
19q13.33
6p12.3
14q23.1
20p13
5q21.1
12q24.33
21q21.1		 TMEM16B
PKP1
SDK2
CALCOCO1
Intergenic
PLEKHG1
CLU
Intergenic
GRM7
Intergenic
Intergenic
TNFRSF21
Intergenic
SMOX
Intergenic
Intergenic
USP25		 rs12579350-?
rs860554-?
rs3816995-?
rs941184-?
rs9302001-?
rs9372078-?
rs17466684-?
rs12061304-?
rs3749380-?
rs2731006-?
rs3810265-?
rs2103868-?
rs4901869-?
rs16989303-?
rs4702982-?
rs7299940-?
rs2823455-?		 0.01
0.05
0.03
0.03
0.20
0.11
0.09
0.10
0.25
0.29
0.07
0.26
0.02
0.21
0.16
0.29
0.03		 4 x 10-9
5 x 10-8
2 x 10-7
3 x 10-7
3 x 10-7
5 x 10-7
7 x 10-7
1 x 10-6
2 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[253,903]		 N
02/25/09 Ling
January 22, 2009
Obesity (Silver Spring)
Genome-wide linkage and association analyses to identify genes influencing adiponectin levels: the GEMS Study. 		Adiponectin levels 997 cases, 989 controls NR 3q27.3
5q35.2		 ADIPOQ
Intergenic		 rs6773957-A
rs7722022-?		 0.37
NR		 5 x 10-8
9 x 10-6 		NR
NR		 Affymetrix
[398,625]		 N
03/03/09 Meyre
January 18, 2009
Nat Genet
Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations. 		Obesity 695 obese adults, 685 obese children, 731 lean adults, 685 lean children 1,171 obese adults, 896 obese children, 1,114 lean adults, 1,297 lean children, 4,417 adults, 5,291 children 16q12.2
18q21.32
16q23.2
10p13
18q11.2		 FTO
MC4R
MAF
PTER
NPC1		 rs1421085-C
rs17782313-C
rs1424233-A
rs10508503-C
rs1805081-A		 0.40
0.18
0.43
0.91
0.56		 1 x 10-28 (children)
5 x 10-15 (children)
4 x 10-13 (children)
2 x 10-7 (children)
3 x 10-7 (children)		 1.39 [1.27-1.51]
1.22 [1.05-1.40]
1.12 [1.00-1.24]
1.56 [1.10-2.78]
1.33 [1.08-1.75]		 Illumina
[308,846]		 N
01/21/09 Tanaka
January 16, 2009
PLoS Genet
Genome-wide association study of plasma polyunsaturated fatty acids in the InCHIANTI Study 		Plasma levels of polyunsaturated fatty acids 1,210 individuals 1,076 individuals NS NS NS NS NS NS Illumina
[495,343]		 N
02/27/09 Carrasquillo
January 11, 2009
Nat Genet
Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease. 		Alzheimer's disease 844 cases, 1,255 controls 1,547 cases, 1,209 controls Xq21.31 PCDH11X rs2573905-? 0.46 2 x 10-7 1.29 [1.17-1.42] Illumina
[313,504]		 N
01/21/09 Burgner
January 09, 2009
PLoS Genet
A genome-wide association study identifies novel and functionally related susceptibility Loci for Kawasaki disease. 		Kawasaki disease 107 cases, 134 controls 583 cases, 1,357 family members 3q26.31
16q22.3		 NAALADL2
ZFHX3		 rs17531088-T
rs7199343-T		 0.44
0.30		 1 x 10-6
2 x 10-6 		1.43 [1.32-1.53]
1.56 [1.33-1.92]		 Affymetrix
[223,922]		 N
02/25/09 Feulner
January 07, 2009
Mol Psychiatry
Examination of the current top candidate genes for AD in a genome-wide association study. 		Alzheimer's disease 491 cases, 479 controls NR 19q13.32 TOMM40, APOE rs157580-? NR 1 x 10-40 NR Illumina
[~550,000]		 N
01/21/09 Ober
January 07, 2009
J Lipid Res
Genome-wide association study of plasma Lp(a)levels Identifies multiple genes on chromosome 6q 		Plasma Lp (a) levels 357 individuals 1,054 individuals 6q25.3 LPA rs6919346-? 0.16 4 x 10-11 .66 [mg/dl decrease] Affymetrix
[290,327]		 N
01/21/09 Silverberg
January 04, 2009
Nat Genet
Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. 		Ulcerative colitis 1,022 cases, 2,503 controls 1,387 cases, 1,115 controls 6p21.32
1p36.13
12q15
1p36.13
1p31.3
1p31.3
12q15
7q31.1
9q21.32
7q31.1
7q31.1
7q31.1		 BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1
OTUD3, PLA2G2E
IFNG, IL26, IL22
RNF186
IL23R
IL23R
IL26
SLC26A3, DLD, LAMB1
Intergenic
Intergenic
SLC26A3, DLD, LAMB1
SLC26A3, DLD, LAMB1		 rs2395185-?
rs6426833-G
rs1558744-A
rs3806308-?
rs10889677-A
rs11209026-?
rs2870946-G
rs4598195-?
rs668853-G
rs4730273-?
rs2158836-A
rs4730276-?		 0.67
0.54
0.38
0.63
0.30
0.93
0.055
0.54
0.39
0.70
0.35
0.39		 1 x 10-16
5 x 10-13
3 x 10-12
7 x 10-9
1 x 10-8
1 x 10-8
5 x 10-7
1 x 10-6
2 x 10-6
5 x 10-6
7 x 10-6
9 x 10-6 		1.52
1.37
1.35
1.28
1.29
1.79
1.54
1.23
1.2
1.22
1.21
1.22 		Illumina
[280,748]		 N
01/21/09 Beecham
January 03, 2009
Am J Hum Genet
Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease. 		Alzheimer's disease 492 cases, 496 controls 238 cases, 220 controls 12q13.11
19q13.31
1q42.2		 FAM113B
ZNF224
DISC1		 rs11610206-?
rs2061333-?
rs12044355-?		 NR
NR
NR		 3 x 10-7
2 x 10-6
9 x 10-6 		NR
NR
NR		 Illumina
[~2.5 million] (imputed)		 N
02/27/09 Hinks
January 01, 2009
Arthritis Rheum
Identification of a novel susceptibility locus for juvenile idiopathic arthritis by genome-wide association analysis. 		Arthritis (juvenile idiopathic) 279 cases, 184 controls up to 654 cases, 1,847 controls 1p13.1 VTCN1 rs12046117-? 0.09 1 x 10-6 1.58 [1.29-1.94] Affymetrix
[88,862]		 N
01/16/09 Limou
January 01, 2009
J Infect Dis
Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). 		AIDS progression 275 HIV positive patients, 1,438 controls 626 patients 6p21.33
6p21.33
6p21.33		 HCP5, MICB, MCCD1, BAT1, LTB, TNF
HLA-C
ZNRD1, RNF39		 rs2395029-G
rs10484554-T
rs8321-G		 0.03
0.13
NR		 3 x 10-19
6 x 10-8
5 x 10-7 		3.47 [2.39-5.04]
NR
NR		 Illumina
[291,119]		 N
02/26/09 Sun
January 01, 2009
Cancer Res
Sequence variants at 22q13 are associated with prostate cancer risk. 		Prostate cancer 1,235 aggressive cases, 1,599 controls 3,629 aggressive cases, 4,255 non-aggressive cases, 5,738 controls 22q13.1 TNRC6B rs9623117-C 0.21 5 x 10-7 1.18 [1.11-1.26] Affymetrix and Illumina
[~2 million] (imputed)		 N
01/14/09 Zhang
December 31, 2008
Mol Psychiatry
Singleton deletions throughout the genome increase risk of bipolar disorder 		Bipolar disorder 1,001 cases, 1,033 controls NR Pending Pending Pending Pending Pending Pending Affymetrix
[51,757 CNVs]		 Y
01/14/09 Wang
December 29, 2008
Proc Natl Acad Sci U S A
From the Cover: Whole-genome association study identifies STK39 as a hypertension susceptibility gene. 		Blood pressure 542 individuals 6,583 individuals 2q24.3 STK39 rs6749447-G 0.28 2 x 10-7 1.9 [1.2-2.6] mm Hg increase in DBP Affymetrix
[79,447]		 N
01/14/09 Meisinger
December 24, 2008
Am J Hum Genet
A genome-wide association study identifies three loci associated with mean platelet volume. 		Mean platelet volume 1,606 individuals 8,617 individuals 12q24.31
17q11.2
3p14.3		 WDR66
TAOK1
ARHGEF3		 rs7961894-A
rs2138852-C
rs12485738-A		 0.11
0.47
0.30		 7 x 10-48
7 x 10-28
4 x 10-27 		.03 [0.03-0.04] per log fl increase
.02 [0.01-0.02] per log fl decrease
.02 [0.01-0.02] per log fl increase		 Affymetrix
[335,152]		 N
02/04/09 Muglia
December 23, 2008
Mol Psychiatry
Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts. 		Major depressive disorder 1,359 cases, 1,782 controls NR 12p13.32 CCND2 rs4238010-G 0.02 6 x 10-6 1.72 Illumina and Affymetrix
[494,678] (imputed)		 N
06/22/09 Pare
December 19, 2008
PLoS Genet
Novel association of HK1 with glycated hemoglobin in a non-diabetic population: a genome-wide evaluation of 14,618 participants in the Women's Genome Health Study. 		Glycated hemoglobin levels 14,618 Caucasian women 455 Caucasian men and women 10q21.3
7p13
2q24.3
8q24.11		 HK1
GCK
G6PC2
SLC30A8		 rs7072268-A
rs730497-A
rs1402837-A
rs13266634-A		 0.50
0.17
0.23
0.30		 2 x 10-25
6 x 10-12
5 x 10-10
5 x 10-8 		.05 [NR] % increase
.03 [NR] % increase
.02 [NR] % increase
.02 [NR] % decrease		 Illumina
[337,343]		 N
01/14/09 Benyamin
December 17, 2008
Am J Hum Genet
Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels. 		Serum markers of iron status 411 family members NR 3q22.1
6q22.33
14q23.2		 TF
RSPO3
Q6ZUR9		 rs1830084-A
rs972275-?
rs973968-?		 0.36
NR
NR		 1 x 10-9 (serum transferrin)
2 x 10-6 (serum ferritin)
3 x 10-6 (transferrin saturation)		 .43 [NR] s.d. increase
NR
NR		 Affymetrix
[100,846]		 N
01/14/09 " Serum markers of iron status 459 twin pairs NR 3q22.1
6p22.1
6p22.1
6p22.1
6p22.1
6p22.1
6p22.2
6p22.2
6p22.2
3q22.1
6q25.3
11p14.3
3q22.1
Xq24
2p14
6p22.1
3q22.1
6p22.2
22q12.3
7p14.1
18q22.2
5p12
5q14.1
6p22.2		 TF
HFE
HFE
HFE
HIST1H2BJ
BTN1A1
LRRC16
SLC17A1
LRRC16
TOPBP1
WTAP
LUZP2
TF
KLHL13
Q6ZNG6
TRIM38
TF
LRRC16A
TMPRSS6
Q4KMW4
Intergenic
GHR
ARSB
SCGN		 rs3811647-?
rs1800562-?
rs1800562-?
rs1800562-?
rs13194491-?
rs13194984-?
rs2274089-?
rs17270561-?
rs2274089-?
rs2718812-?
rs4516970-?
rs10500991-?
rs1867504-?
rs2430212-?
rs1457451-?
rs12216125-?
rs1799852-?
rs2274089-?
rs4820268-?
rs29880-?
rs2660917-?
rs13188386-?
rs2052550-?
rs932316-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
0.09
NR
NR
NR
NR
NR
NR
NR		 3 x 10-15 (serum transferrin)
4 x 10-15 (transferrin saturation)
4 x 10-11 (serum iron)
1 x 10-10 (serum transferrin)
1 x 10-8 (transferrin saturation)
6 x 10-8 (transferrin saturation)
3 x 10-7 (serum transferrin)
5 x 10-7 (transferrin saturation)
8 x 10-7 (transferrin saturation)
1 x 10-6 (serum transferrin)
1 x 10-6 (serum ferritin)
2 x 10-6 (serum transferrin)
2 x 10-6 (serum transferrin)
2 x 10-6 (serum transferrin)
3 x 10-6 (transferrin saturation)
4 x 10-6 (transferrin saturation)
5 x 10-6 (serum transferrin)
5 x 10-6 (serum iron)
6 x 10-6 (serum iron)
7 x 10-6 (serum ferritin)
8 x 10-6 (serum ferritin)
8 x 10-6 (transferrin saturation)
8 x 10-6 (serum ferritin)
9 x 10-6 (transferrin saturation)		 .46 [0.34-0.58] s.d. decrease
NR
.66 [0.46-0.86] s.d. increase
.68 [0.48-0.88] s.d. decrease
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
.43 [0.25-0.61] s.d. decrease
NR
NR
NR
NR
NR
NR
NR		 Illumina
[315,887]		 N
01/14/09 Pollin
December 17, 2008
Science
A null mutation in human APOC3 confers a favorable plasma lipid profile and apparent cardioprotection. 		Triglycerides 809 individuals 698 individuals 11q23.3 APOA1, APOC3, APOA4, APOA5, DSCAML1 rs10892151-A 0.028 3 x 10-29 NR Affymetrix
[381,934]		 N
01/16/09 Styrkarsdottir
December 14, 2008
Nat Genet
New sequence variants associated with bone mineral density. 		Bone mineral density (hip) 6,865 individuals 8,510 individuals 1p36.12
6q25.1
17q21.31
11p11.2
17q21.31
Xq21.2
2q12.1
3p22.1		 Intergenic
ESR1
SOST
LRP4
C17orf53
NR
NR
NR		 rs7524102-A
rs1038304-G
rs1513670-A
rs1007738-A
rs227584-T
rs2710057-T
rs6735786-C
rs10490823-G		 0.82
0.47
0.37
0.77
0.73
0.67
0.64
0.46		 1 x 10-16
4 x 10-10
2 x 10-8
7 x 10-7
9 x 10-7
1 x 10-6
2 x 10-6
9 x 10-6 		.15 [0.11-0.18] s.d. decrease
.08 [0.06-0.11] s.d. decrease
.08 [0.05-0.10] s.d. decrease
.08 [0.05-0.11] s.d. decrease
.07 [0.04-0.10] s.d. decrease
.07 [0.04-0.09] s.d. decrease
.07 [0.04-0.09] s.d. decrease
.06 [0.03-0.09] s.d. decrease		 Illumina
[305,051]		 N
01/16/09 " Bone mineral density (spine) 6,865 individuals 8,510 individuals 13q14.11
6q25.1
1p36.12
12q13.13
2p16.2
2p22.2
21q11.2		 RANKL
C6orf97, ESR1
Intergenic
OSX
SPTBN1
LOC344382
NR		 rs9594759-T
rs6929137-A
rs6696981-G
rs10876432-A
rs11898505-G
rs4670779-T
rs1006899-A		 0.62
0.30
0.86
0.73
0.68
0.32
0.84		 2 x 10-17
2 x 10-10
2 x 10-8
1 x 10-7
4 x 10-6
4 x 10-6
6 x 10-6 		.12 [0.09-0.15] s.d. decrease
.1 [0.07-0.13] s.d. decrease
.12 [0.08-0.16] s.d. decrease
.08 [0.05-0.11] s.d. decrease
.07 [0.04-0.10] s.d. decrease
.07 [0.04-0.10] s.d. decrease
.09 [0.05-0.13] s.d. decrease		 Illumina
[305,051]		 N
01/15/09 Thorleifsson
December 14, 2008
Nat Genet
Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. 		Body mass index 80,969 individuals 11,036 individuals 16q12.2
2p25.3
16q12.2
18q21.32
19q13.11
1p31.1
3q27.2
16p11.2
11p14.1
11p14.1
1q25.2
12q13.13
1p21.3
11p14.1		 FTO
TMEM18
FTO
MC4R
KCTD15, CHST8
NEGR1
SFRS10, ETV5, DGKG
SH2B1, ATP2A1
BDNF
BDNF
SEC16B, RASAL2
BCDIN3D, FAIM2
NR
BDNF		 rs8050136-A
rs7561317-G
rs6499640-A
rs12970134-A
rs29941-C
rs2568958-A
rs7647305-C
rs7498665-G
rs6265-G
rs925946-T
rs10913469-C
rs7138803-A
rs10783050-C
rs7481311-T		 0.41
0.84
0.41
0.30
0.69
0.58
0.77
0.44
0.85
0.34
0.20
0.37
0.36
0.24		 1 x 10-47
4 x 10-17
4 x 10-13
1 x 10-12
7 x 10-12
1 x 10-11
7 x 10-11
3 x 10-10
5 x 10-10
9 x 10-10
6 x 10-8
1 x 10-7
4 x 10-6
8 x 10-6 		8.04 [6.96-9.12] % SD
6.12 [4.69-7.55] % SD
5.25 [3.82-6.68] % SD
4.38 [3.16-5.60] % SD
4.18 [2.98-5.38] % SD
3.77 [2.67-4.87] % SD
4.42 [3.09-5.75] % SD
3.63 [2.49-4.77] % SD
4.58 [3.07-6.09] % SD
3.85 [2.62-5.08] % SD
3.36 [2.14-4.58] % SD
3.28 [2.06-4.50] % SD
2.6 [1.50-3.70] % SD
3.15 [1.78-4.52] % SD		 Illumina
[305,846]		 N
01/15/09 " Weight 80,969 individuals 11,036 individuals 16q12.2
2p25.3
16q12.2
18q21.32
16p11.2
11p14.1
3q27.2
19q13.11
1q25.2
1p31.1
6p21.33
11p14.1
12q13.13
13q12.2
1p21.3
5q23.2
11p14.1		 FTO
TMEM18
FTO
MC4R
SH2B1, ATP2A1
BDNF
SFRS10, ETV5, DGKG
KCTD15, CHST8
SEC16B, RASAL2
NEGR1
AIF1, NCR3
BDNF
BCDIN3D, FAIM2
NR
NR
NR
BDNF		 rs8050136-A
rs7561317-G
rs6499640-A
rs12970134-A
rs7498665-G
rs925946-T
rs7647305-C
rs29941-C
rs10913469-C
rs2568958-A
rs2844479-T
rs6265-G
rs7138803-A
rs7336332-G
rs1973993-C
rs2115172-A
rs7481311-T		 0.41
0.84
0.65
0.30
0.44
0.34
0.77
0.69
0.20
0.58
0.68
0.85
0.37
0.15
0.63
0.57
0.24		 5 x 10-36
2 x 10-18
6 x 10-14
5 x 10-13
1 x 10-9
4 x 10-9
4 x 10-9
5 x 10-9
1 x 10-8
2 x 10-8
2 x 10-8
2 x 10-7
2 x 10-7
1 x 10-6
1 x 10-6
2 x 10-6
3 x 10-6 		7.05 [5.95-8.15] % SD
6.47 [5.02-7.92] % SD
5.5 [4.07-6.93] % SD
4.66 [3.41-5.91] % SD
3.69 [2.51-4.87] % SD
3.8 [2.55-5.05] % SD
4 [2.67-5.33] % SD
3.73 [2.48-4.98] % SD
3.82 [2.51-5.13] % SD
3.37 [2.19-4.55] % SD
3.58 [2.33-4.83] % SD
4 [2.47-5.53] % SD
3.27 [2.05-4.49] % SD
4.01 [2.40-5.62] % SD
2.71 [1.61-3.81] % SD
2.71 [1.59-3.83] % SD
3.5 [2.03-4.97] % SD		 Illumina
[305,846]		 N
01/12/09 Willer
December 14, 2008
Nat Genet
Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. 		Body mass index 32,387 individuals 59,092 individuals 16q12.2
2p25.3
18q21.32
4p13
16p11.2
11p11.2
19q13.11
1p31.1
11p15.4
20p12.3
15q25.2		 FTO
TMEM18
MC4R
GNPDA2
SH2B1
MTCH2
KCTD15
NEGR1
STK33
BMP2
RKHD3		 rs9939609-A
rs6548238-C
rs17782313-C
rs10938397-G
rs7498665-G
rs10838738-G
rs11084753-G
rs2815752-A
rs10769908-C
rs2145270-T
rs12324805-C		 0.41
0.84
0.21
0.45
0.41
0.34
0.67
0.62
0.53
0.65
0.31		 4 x 10-51
1 x 10-18
5 x 10-18
3 x 10-16
5 x 10-11
5 x 10-9
2 x 10-8
6 x 10-8
1 x 10-6
6 x 10-6
7 x 10-6 		.33 [0.27-0.39] kg/m2 increase
.26 [0.19-0.34] kg/m2 increase
.2 [0.12-0.28] kg/m2 increase
.19 [0.13-0.25] kg/m2
.15 [0.08-0.21] kg/m2 increase
.07 [0.01-0.13] kg/m2 increase
.06 [-0.01-0.13] kg/m2 increase
.1 [0.04-0.16] kg/m2 increase
NR
NR
NR		 Illumina and Affymetrix
[2,399,588] (imputed)		 N
02/05/09 Mead
December 11, 2008
Lancet Neurol
Genetic risk factors for variant Creutzfeldt-Jakob disease: a genome-wide association study. 		Creutzfeldt-Jakob disease 117 CJD cases, 3,083 controls 506 sCJD cases, 28 iCJD cases, 151 Kuru cases, 125 Kuru-resistant cases, up to 1,137 controls 20p13
8q21.13		 PRNP
STMN2		 rs1799990-A
rs1460163-A		 NR
NR		 2 x 10-21
6 x 10-8 		NR
NR		 Affymetrix
[288,908]		 N
01/06/09 Sullivan
December 09, 2008
Mol Psychiatry
Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo 		Major depressive disorder 1,738 cases, 1,802 controls 6,079 cases, 5,893 controls NS NS NS NS NS NS Perlegen
[435,291]		 N
01/12/09 Aulchenko
December 07, 2008
Nat Genet
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. 		Cholesterol, total 22,562 individuals NR 19p13.2
2p24.1
1p13.3
19q13.32
5q13.3
19p13.11
1p31.3
18q21.1
2p21
11q12.2
1p36.11
8q24.13
15q22.1
11q23.3
7p15.3		 LDLR
APOB
CELSR2
TOMM40, APOE
HMGCR
NCAN
DOCK7
LIPG
ABCG5
FADS2, FADS3
TMEM57
TRIB1
LIPC
APOA1, APOA4, APOA5, APOC3
DNAH11		 rs2228671-G
rs693-G
rs646776-G
rs2075650-G
rs3846662-G
rs2304130-G
rs10889353-C
rs4939883-G
rs6756629-G
rs174570-G
rs10903129-G
rs6987702-G
rs1532085-G
rs12272004-C
rs12670798-G		 0.88
0.52
0.22
0.15
0.44
0.07
0.32
0.83
0.92
0.83
0.54
0.29
0.59
0.93
0.24		 9 x 10-24
9 x 10-23
9 x 10-22
3 x 10-19
3 x 10-19
2 x 10-15
4 x 10-12
2 x 10-11
2 x 10-11
2 x 10-10
5 x 10-10
3 x 10-9
4 x 10-7
7 x 10-7
9 x 10-7 		.16 [NR] s.d. increase
.1 [NR] s.d. decrease
.13 [NR] s.d. decrease
.14 [NR] s.d. increase
.09 [NR] s.d. increase
.15 [NR] s.d. decrease
.08 [NR] s.d. decrease
.07 [NR] s.d. increase
.15 [NR] s.d. increase
.09 [NR] s.d. increase
.06 [NR] s.d. increase
.07 [NR] s.d. increase
.05 [NR] s.d. decrease
.11 [NR] s.d. decrease
.06 [NR] s.d. increase		 Illumina and Affymetrix
[up to ~600,000]		 N
01/12/09 " HDL cholesterol 21,412 individuals NR 16q13
15q22.1
8p21.3
16q22.1
9q31.1
18q21.1
11p11.2
2p24.1
19q13.32
11q12.2		 CETP
LIPC
LPL
CTCF, PRMT8
ABCA1
LIPG
MADD, FOLH1
APOB
TOMM40, APOE
FADS2, FADS3		 rs1532624-C
rs1532085-G
rs2083637-G
rs2271293-G
rs3905000-G
rs4939883-G
rs7395662-G
rs6754295-C
rs157580-G
rs174570-G		 0.57
0.59
0.26
0.87
0.86
0.83
0.61
0.25
0.33
0.83		 9 x 10-94
1 x 10-35
6 x 10-18
8 x 10-16
9 x 10-13
2 x 10-11
6 x 10-11
4 x 10-8
4 x 10-7
4 x 10-6 		.21 [NR] s.d. decrease
.13 [NR] s.d. decrease
.11 [NR] s.d. increase
.13 [NR] s.d. decrease
.11 [NR] s.d. increase
.1 [NR] s.d. increase
.07 [NR] s.d. decrease
.07 [NR] s.d. increase
.06 [NR] s.d. increase
.06 [NR] s.d. increase		 Illumina and Affymetrix
[up to ~600,000]		 N
01/12/09 " LDL cholesterol 17,797 individuals NR 1p13.3
19q13.32
2p24.1
19p13.2
11q12.2
11q23.3
5q13.3
2p21
7p15.3
19p13.11
8q24.13
1p31.3		 CELSR2
TOMM40, APOE
APOB
LDLR
FADS2, FADS3
APOA1, APOA4, APOA5, APOC3
HMGCR
ABCG5
DNAH11
NCAN
TRIB1
DOCK7		 rs646776-G
rs157580-G
rs693-G
rs2228671-G
rs174570-G
rs12272004-C
rs3846662-G
rs6756629-G
rs12670798-G
rs2304130-G
rs6987702-G
rs10889353-C		 0.22
0.33
0.52
0.88
0.83
0.93
0.44
0.92
0.24
0.07
0.29
0.32		 8 x 10-23
2 x 10-19
4 x 10-17
4 x 10-14
4 x 10-13
5 x 10-13
2 x 10-11
3 x 10-10
6 x 10-9
3 x 10-6
3 x 10-6
8 x 10-6 		.16 [NR] s.d. decrease
.11 [NR] s.d. decrease
.1 [NR] s.d. decrease
.14 [NR] s.d. increase
.11 [NR] s.d. increase
.18 [NR] s.d. decrease
.08 [NR] s.d. increase
.16 [NR] s.d. increase
.09 [NR] s.d. increase
.12 [NR] s.d. decrease
.07 [NR] s.d. increase
.06 [NR] s.d. decrease		 Illumina and Affymetrix
[up to 600,000]		 N
01/12/09 " Triglycerides 17,815 individuals NR 2p23.3
8p21.3
11q23.3
7q11.23
1p31.3
19q13.32
2p24.1
19p13.11		 GCKR
LPL
APOA1, APOA4, APOA5, APOC3
MLXIPL
DOCK7
TOMM40, APOE
APOB
NCAN		 rs780094-G
rs10096633-G
rs12272004-C
rs2240466-G
rs1167998-C
rs439401-G
rs6754295-C
rs2304130-G		 0.63
0.88
0.93
0.87
0.32
0.68
0.25
0.07		 3 x 10-20
2 x 10-18
5 x 10-13
1 x 10-12
2 x 10-12
2 x 10-9
3 x 10-8
3 x 10-6 		.1 [NR] s.d. decrease
.17 [NR] s.d. increase
.18 [NR] s.d. decrease
.14 [NR] s.d. increase
.09 [NR] s.d. decrease
.09 [NR] s.d. increase
.08 [NR] s.d. decrease
.1 [NR] s.d. decrease		 Illumina and Affymetrix
[up to 600,000]		 N
01/07/09 Bouatia-Naji
December 07, 2008
Nat Genet
A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk. 		Fasting plasma glucose 2,151 individuals 6,332 cases, 9,132 controls 11q21 MTNR1B rs1387153-T 0.29 2 x 10-36 .07 [0.05-0.08] mmol/l increase Illumina
[308,846]		 N
01/12/09 Kathiresan
December 07, 2008
Nat Genet
Common variants at 30 loci contribute to polygenic dyslipidemia. 		HDL cholesterol 19,840 individuals Up to 20,623 individuals 16q13
8p21.3
15q22.1
18q21.1
16q22.1
11q23.3
11q12.2
12q24.11
9p22.3
20q13.12
9q31.1
20q13.12
19p13.2
1q42.13		 CETP
LPL
LIPC
LIPG
LCAT
APOA1, APOC3, APOA4, APOA5
FADS1, FADS2, FADS3
MMAB,MVK
TTC39B
HNF4A
ABCA1
PLTP
ANGPTL4
GALNT2		 rs173539-T
rs12678919-G
rs10468017-T
rs4939883-T
rs2271293-A
rs964184-G
rs174547-C
rs2338104-C
rs471364-C
rs1800961-T
rs1883025-T
rs7679-C
rs2967605-T
rs4846914-G		 0.32
0.10
0.30
0.17
0.11
0.14
0.33
0.45
0.12
0.03
0.26
0.19
0.16
0.40		 4 x 10-75
2 x 10-34
8 x 10-23
7 x 10-15
9 x 10-13
1 x 10-12
2 x 10-12
1 x 10-10
3 x 10-10
8 x 10-10
1 x 10-9
4 x 10-9
1 x 10-8
4 x 10-8 		.25 [0.21-0.29] s.d. increase
.23 [0.17-0.29] s.d. increase
.1 [0.06-0.14] s.d. increase
.14 [0.10-0.18] s.d. decrease
.07 [0.01-0.13] s.d. increase
.17 [0.11-0.23] s.d. decrease
.09 [0.05-0.13] s.d. decrease
.07 [0.03-0.11] s.d. decrease
.08 [0.02-0.14] s.d. decrease
.19 [0.09-0.29] s.d. decrease
.08 [0.04-0.12] s.d. decrease
.07 [0.03-0.11] s.d. decrease
.12 [0.04-0.20] s.d. decrease
.05 [0.01-0.09] s.d. decrease		 Affymetrix and Illumina
[~2,600,000] (imputed)		 N
01/12/09 " LDL cholesterol 19,840 individuals Up to 20,623 individuals 1p13.3
2p24.1
19q13.32
19p13.2
2p21
5q13.3
5q33.3
20q12
12q24.31
19p13.11
1p32.3		 CELSR2, PSRC1, SORT1
APOB
APOE, APOC1, APOC4, APOC2
LDLR
ABCG8
HMGCR
TIMD4, HAVCR1
MAFB
HNF1A
NCAN, CILP2, PBX4
PCSK9		 rs12740374-T
rs515135-T
rs4420638-G
rs6511720-T
rs6544713-T
rs3846663-T
rs1501908-G
rs6102059-T
rs2650000-A
rs10401969-C
rs11206510-C		 0.21
0.20
0.16
0.10
0.32
0.38
0.37
0.32
0.36
0.06
0.19		 2 x 10-42
5 x 10-29
4 x 10-27
2 x 10-26
2 x 10-20
8 x 10-12
1 x 10-11
4 x 10-9
2 x 10-8
2 x 10-8
4 x 10-8 		.23 [0.19-0.27] s.d. decrease
.16 [0.12-0.20] s.d. decrease
.29 [0.17-0.41] s.d. increase
.26 [0.18-0.34] s.d. increase
.15 [0.11-0.19] s.d. increase
.07 [0.03-0.11] s.d. increase
.07 [0.03-0.11] s.d. decrease
.06 [0.03-0.10] s.d. decrease
.07 [0.03-0.11] s.d. increase
.05 [-0.03-0.13] s.d. decrease
.09 [0.05-0.13] s.d. decrease		 Affymetrix and Illumina
[~2,600,000] (imputed)		 N
01/12/09 " Triglycerides 19,840 individuals Up to 20,623 individuals 11q23.3
8p21.3
2p23.3
8q24.13
7q11.23
11q12.2
2p24.1
19p13.11
20q13.12
8p23.1
1p31.3		 APOA1, APOC3, APOA4, APOA5
LPL
GCKR
TRIB1
MLXIPL
FADS1, FADS2, FADS3
APOB
NCAN,CILP2,PBX4
PLTP
XKR6, AMAC1L2
ANGPTL3		 rs964184-G
rs12678919-G
rs1260326-T
rs2954029-T
rs714052-G
rs174547-C
rs7557067-G
rs17216525-T
rs7679-C
rs7819412-G
rs10889353-C		 0.14
0.10
0.45
0.44
0.12
0.33
0.22
0.07
0.19
0.48
0.33		 4 x 10-62
2 x 10-41
2 x 10-31
3 x 10-19
3 x 10-15
2 x 10-14
9 x 10-12
4 x 10-11
7 x 10-11
3 x 10-8
3 x 10-7 		.3 [0.24-0.36] s.d. increase
.25 [0.19-0.31] s.d. decrease
.12 [0.08-0.16] s.d. increase
.11 [0.07-0.15] s.d. decrease
.16 [0.10-0.22] s.d. decrease
.06 [0.02-0.10] s.d. increase
.08 [0.04-0.12] s.d. decrease
.11 [0.05-0.17] s.d. decrease
.07 [0.03-0.11] s.d. increase
.04 [0.001-0.08] s.d. decrease
.05 [0.01-0.09] s.d. decrease		 Affymetrix and Illumina
[~2,600,000] (imputed)		 N
01/12/09 Sabatti
December 07, 2008
Nat Genet
Genome-wide association analysis of metabolic traits in a birth cohort from a founder population. 		HDL cholesterol 4,763 individuals NR 16q13
15q22.1
16q22.1
11p11.2
17p13.3		 CETP
LIPC
LCAT
NR1H3
Intergenic		 rs3764261-A
rs1532085-A
rs255049-G
rs7120118-G
rs9891572-A		 0.28
0.44
0.22
0.42
0.16		 7 x 10-29
2 x 10-10
3 x 10-8
4 x 10-8
2 x 10-7 		.09 [0.08-0.11] mmol/l increase
.05 [0.03-0.06] mmol/l increase
.05 [0.03-0.07] mmol/l increase
.04 [0.03-0.05] mmol/l increase
.05 [0.048-0.051] mmol/l increase		 Illumina
[329,091]		 N
01/12/09 " LDL cholesterol 4,763 individuals NR 1p13.3
2p24.1
19q13.32
11q12.2
19p13.2
1q32.2
Xq12		 CELSR2, PSRC1, SORT1
APOB
APO cluster
FADS1, FADS2
LDLR
CR1L
AR		 rs646776-G
rs693-A
rs157580-G
rs174546-A
rs11668477-G
rs4844614-A
rs5031002-A		 0.21
0.41
0.29
0.44
0.18
0.32
0.02		 2 x 10-12
3 x 10-11
5 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
2 x 10-7 		.16 [0.11-0.20] mmol/l decrease
.12 [0.09-0.16] mmol/l increase
.11 [0.07-0.15] mmol/l decrease
.1 [0.06-0.13] mmol/l decrease
.13 [0.08-0.17] mmol/l decrease
.1 [0.06-0.14] mmol/l increase
.3 [0.18-0.41] mmol/l increase		 Illumina
[329,091]		 N
01/12/09 " Other metabolic traits 4,763 individuals NR 1q23.2
12q24.31
2p23.3
2q24.3
2p24.1
8p21.3
11q21
7p21.2
10q23.31
15q14
1p31.3		 CRP
LEF1
GCKR
G6PC2, ABCB11
APOB
LPL
MTNR1B
Intergenic
PANK1
Intergenic
LEPR		 rs2794520-A
rs2650000-A
rs1260326-A
rs560887-A
rs673548-A
rs10096633-A
rs1447352-G
rs10244051-C
rs11185790-A
rs2624265-G
rs12753193-G		 0.36
0.45
0.35
0.31
0.27
0.098
0.42
0.46
0.21
0.42
0.45		 3 x 10-22 (CRP)
3 x 10-11 (CRP)
4 x 10-10 (TG)
6 x 10-10 (GLU)
2 x 10-8 (TG)
5 x 10-8 (TG)
6 x 10-8 (GLU)
1 x 10-7 (GLU)
3 x 10-7 (INS)
4 x 10-7 (TG)
4 x 10-7 (CRP)		 .47 [0.32-0.62] mmol/l decrease
.4 [0.25-0.55] mmol/l decrease
.09 [0.06-0.12] mmol/l increase
.06 [0.04-0.07] mmol/l decrease
.08 [0.05-0.11] mmol/l decrease
.12 [0.07-0.17] mmol/l decrease
.05 [0.03-0.06] mmol/l decrease
.05 [0.03-0.06] mmol/l increase
.31 [0.18-0.44] mmol/l decrease
.07 [0.04-0.10] mmol/l increase
.13 [-0.02-0.27] mmol/l decrease		 Illumina
[329,091]		 N
05/07/09 Lasky-Su
December 05, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations. 		Attention deficit hyperactivity disorder 909 trios NR 12p11.22
3p24.3
14q23.2
2q21.2
16q22.1
13q32.3
1q41
22q12.3
2q24.1
1p31.2
2p21
3p14.1
11p13
19q13.43
3p14.2
4q13.3
2q14.1
2q14.3
8q24.3		 Intergenic
Intergenic
Intergenic
FLJ34870
HAS3
CLYBL
Intergenic
Intergenic
Intergenic
Intergenic
OXER1
FOXP1
Intergenic
ZNF544
FHIT
EREG
Intergenic
Intergenic
NAPRT1		 rs522958-?
rs11719664-?
rs1514928-?
rs7577925-?
rs8047014-?
rs7992643-?
rs1018040-?
rs130575-?
rs1918172-?
rs4147141-?
rs930421-?
rs17651978-?
rs10767942-?
rs260461-?
rs6791644-?
rs1350666-?
rs272000-?
rs17367118-?
rs2290416-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-6 (binary)
2 x 10-6 (count)
3 x 10-6 (binary)
3 x 10-6 (binary)
4 x 10-6 (binary)
5 x 10-6 (count)
5 x 10-6 (binary)
5 x 10-6 (binary)
5 x 10-6 (count)
6 x 10-6 (count)
6 x 10-6 (binary)
6 x 10-6 (count)
8 x 10-6 (count)
8 x 10-6 (binary)
8 x 10-6 (count)
8 x 10-6 (binary)
9 x 10-6 (count)
9 x 10-6 (count)
9 x 10-6 (count)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
05/07/09 " Hyperactive-impulsive symptoms 909 trios NR 12p11.22
6p22.3
2p21
8p21.3
1p13.2
15q14
21q21.3
3q26.1
9p24.3
19q13.43
1q41
3q26.1
18q22.1
6p22.3		 Intergenic
Intergenic
OXER1
LPL
Intergenic
MEIS2
GRIK1
Intergenic
DMRT2
LOC390980
Intergenic
Intergenic
Intergenic
Intergenic		 rs522958-?
rs41441749-?
rs6719977-?
rs7816032-?
rs11590090-?
rs8041675-?
rs363512-?
rs6808138-?
rs17641078-?
rs2014572-?
rs1018040-?
rs6808138-?
rs13353224-?
rs1202199-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 8 x 10-7 (binary)
1 x 10-6 (binary)
2 x 10-6 (binary)
2 x 10-6 (count)
3 x 10-6 (count)
4 x 10-6 (count)
4 x 10-6 (binary)
5 x 10-6 (binary)
5 x 10-6 (binary)
7 x 10-6 (count)
8 x 10-6 (binary)
8 x 10-6 (binary)
9 x 10-6 (count)
9 x 10-6 (count)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
05/07/09 " Inattentive symptoms 909 trios NR 9q22.32
8q21.11
11q22.3
15q26.1
16q12.1
9q21.31
15q25.1
7q36.3
13q12.12
1p31.2
12q24.22
15q13.1
1p31.2
16q23.1
8p11.21		 Intergenic
Intergenic
Intergenic
SLCO3A1
ZNF423
Intergenic
IL16
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic		 rs11790994-?
rs12679254-?
rs10895959-?
rs7495052-?
rs17281813-?
rs2769967-?
rs7172689-?
rs10227331-?
rs17079773-?
rs4650135-?
rs478597-?
rs1471225-?
rs4147141-?
rs13330107-?
rs11786458-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7 (binary)
2 x 10-6 (binary)
3 x 10-6 (binary)
3 x 10-6 (binary)
3 x 10-6 (binary)
3 x 10-6 (count)
4 x 10-6 (count)
4 x 10-6 (count)
5 x 10-6 (binary)
5 x 10-6 (binary)
8 x 10-6 (binary)
8 x 10-6 (count)
8 x 10-6 (binary)
9 x 10-6 (binary)
9 x 10-6 (binary)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
05/07/09 Lasky-Su
December 05, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association scan of the time to onset of attention deficit hyperactivity disorder. 		Attention deficit hyperactivity disorder (time to onset) 930 trios NR 6q15
2q36.3
7q31.1
11p15.1
3p22.3
9p23
3q29
20q13.13
14q23.1
5q35.3
8q23.3		 Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
SULF2
Intergenic
ADAMTS2
Intergenic		 rs806276-A
rs1517484-C
rs6968385-T
rs874426-C
rs9845475-G
rs1325154-C
rs3892715-C
rs4810685-C
rs1335515-C
rs10039254-A
rs17658378-A		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 3 x 10-7 (later onset)
5 x 10-7 (earlier onset)
2 x 10-6 (earlier onset)
4 x 10-6 (earlier onset)
4 x 10-6 (later onset)
5 x 10-6 (later onset)
6 x 10-6 (earlier onset)
7 x 10-6 (earlier onset)
8 x 10-6 (earlier onset)
8 x 10-6 (later onset)
9 x 10-6 (later onset)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[429,981]		 N
01/15/09 Timpson
December 03, 2008
Diabetes
Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data. 		Type 2 diabetes 1,924 cases, 2,938 controls 3,757 cases, 5,346 controls 10q25.2
16q12.2
10q25.2
11p15.1
11p15.1
6p22.3
9p21.3
8q24.11		 TCF7L2
FTO
TCF7L2
KCNJ11
KCNJ11
CDKAL
CDKN2B
SLC30A8		 rs7903146-?
rs8050136-?
rs7903146-?
rs5219-?
rs5219-?
rs10946398-?
rs10811661-?
rs13266634-?		 NR
NR
NR
NR
NR
NR
NR
NR		 9 x 10-30 (non-obese)
2 x 10-17 (obese)
6 x 10-16 (obese)
1 x 10-9 (non-obese)
5 x 10-7 (obese)
7 x 10-7 (non-obese)
7 x 10-7 (non-obese)
7 x 10-6 (non-obese)		 1.49 [1.39-1.59]
1.3 [1.23-1.39]
1.31 [1.23-1.40]
1.25 [1.16-1.34]
1.19 [1.11-1.27]
1.18 [1.11-1.26]
1.26 [1.15-1.38]
1.18 [1.10-1.27]		 Affymetrix
[393,453]		 N
01/12/09 Friedman
December 01, 2008
Hum Mol Genet
grm7 variants confer susceptibility to age-related hearing impairment 		Hearing impairment 846 cases, 846 controls 63 cases, 67 controls NS NS NS NS NS NS Affymetrix
[506,627] (pooled)		 N
02/26/09 Prokopenko
December 01, 2008
Nat Genet
Variants in MTNR1B influence fasting glucose levels. 		Fasting plasma glucose 35,812 individuals NR 2q24.3
11q21
7p13		 G6PC2
MTNR1B
GCK		 rs560887-C
rs10830963-G
rs4607517-A		 0.70
0.28
0.18		 1 x 10-57
3 x 10-50
1 x 10-25 		.06 [0.05-0.07] mmol/l increase
.07 [0.06-0.08] mmol/l increase
.06 [0.05-0.07] mmol/l increase		 Affymetrix, Illumina and Perlegen
[up to 2,557,249] (imputed)		 N
12/24/08 Gieger
November 28, 2008
PLoS Genet
Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. 		Serum metabolites 284 males NR 2p14
10p11.21
11q12.2
13q31.3
15q22.1
3p25.3
6q25.1
6q26
15q26.1
4q13.1
7q31.1
12q24.21
6q12
3q28
16p13.2
3q22.3		 PLEK
ANKRD30A
FADS1
GPC5
LIPC
ATP2B2
C6orf71
PARK2
SV2B
Intergenic
Intergenic
Intergenic
Intergenic
FGF12
A2BP1
Intergenic		 rs9309413-?
rs1148259-?
rs174548-?
rs17267292-?
rs4775041-?
rs6807064-?
rs1591830-?
rs992037-?
rs886144-?
rs10517480-?
rs10953730-?
rs2194980-?
rs9354308-?
rs4453795-?
rs9924951-?
rs1382269-?		 0.45
0.42
0.28
0.28
0.28
0.29
0.32
0.35
0.38
0.31
0.35
0.33
0.37
0.41
0.41
0.47		 2 x 10-9 (SM)
3 x 10-9 (SM)
5 x 10-8 (PC)
1 x 10-7 (Docosahexaonic acid)
1 x 10-7 (PE)
1 x 10-7 (phenylalanine)
1 x 10-7 (sugar)
1 x 10-7 (Lysine)
2 x 10-7 (SM)
2 x 10-7 (PC)
2 x 10-7 (acylcarnitine)
3 x 10-7 (Tyrosine)
3 x 10-7 (serotonin)
4 x 10-7 (PC)
5 x 10-7 (PC)
5 x 10-7 (SM)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[187,454]		 N
12/09/08 Terracciano
November 24, 2008
Mol Psychiatry
Genome-wide association scan for five major dimensions of personality. 		Personality dimensions 3,972 individuals 3,903 individuals 19q13.31
4q12
2p22.1
Xp11.3
19q13.31		 ZNF180
CLOCK
THUMPD2
FUNDC1
ZNF180		 rs644148-G
rs6832769-A
rs2540226-T
rs6610953-G
rs644148-G		 0.50
0.73
0.53
0.85
0.50		 9 x 10-7 (openness)
2 x 10-6 (agreeableness)
3 x 10-6 (agreeableness)
6 x 10-6 (openness)
8 x 10-6 (extraversion)		 .15 [NR] s.d. increase
.14 [NR] s.d. decrease
.13 [NR] s.d. increase
.15 [NR] s.d. increase
.14 [NR] s.d. increase		 Affymetrix
[362,129]		 N
01/07/09 Lei
November 23, 2008
Hum Genet
Genome-wide association scan for stature in Chinese: evidence for ethnic specific loci. 		Height 618 Chinese individuals 2,953 Chinese individuals 9q22.23 ZNP510 rs10816533-C 0.29 2 x 10-6 NR Affymetrix
[281,533]		 N
01/06/09 Potkin
November 20, 2008
Schizophr Bull
A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype. 		Brain imaging in schizophrenia (interaction) 64 cases, 74 cases NR 5q23.2
2q37.3
3p12.3
14q32.32
3q26.2
6q16.2		 CTXN3, SLC12A2
GPC1
ROBO2, ROBO1
TRAF3
TNIK
POU3F2		 rs245201-?
rs1574192-?
rs9836484-?
rs10133111-?
rs2088885-?
rs9491640-?		 0.32
0.38
0.32
0.20
0.47
0.06		 9 x 10-8
4 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR		 Illumina
[302,783]		 N
12/01/08 COGENT Study
November 16, 2008
Nat Genet
Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. 		Colorectal cancer 1,902 cases, 1,929 controls 4,878 cases, 4,914 controls 20p12.3
14q22.2
19q13.11
16q22.1		 Intergenic
BMP4
RHPN2
CDH1		 rs961253-A
rs4444235-C
rs10411210-C
rs9929218-A		 0.36
0.46
0.90
0.29		 2 x 10-10
8 x 10-10
5 x 10-9
1 x 10-8 		1.12 [1.08-1.16]
1.11 [1.08-1.15]
1.15 [1.10-1.20]
1.1 [1.06-1.12]		 Illumina
[up to 548,586]		 N
01/16/09 Baranzini
November 14, 2008
Hum Mol Genet
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. 		Brain lesion load 791 cases, 883 controls NR 2q37.1
14q12
19p13.11
6q25.3		 CHRND
NUBPL
CPAMD8
IGF2R		 rs2602397-?
rs2039485-?
rs11666377-?
rs6917747-?		 0.45
0.22
0.14
0.15		 4 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6 		NR
NR
NR
NR		 Illumina
[551,642]		 N
01/16/09 " Multiple sclerosis 978 cases, 883 controls NR 20p13
13q31.3
12q12
8p23.2
3q23
9p22.2
2q14.2
3q24
4q35.1
2p25.1		 C20orf46
GPC5
PDZRN4
CSMD1
SLC25A36
SH3GL2
EN1
ZIC1
MGC45800
DDEF2		 rs397020-?
rs9523762-?
rs1458175-?
rs1529316-?
rs908821-?
rs1755289-?
rs651477-?
rs1841770-?
rs7672826-?
rs1109670-?		 0.52
0.35
0.49
0.47
0.71
0.61
0.26
0.53
0.34
0.26		 8 x 10-7
1 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6 		1.41 [NR]
1.36 [NR]
1.34 [NR]
1.36 [NR]
1.37 [NR]
1.35 [NR]
1.38 [NR]
1.34 [NR]
1.37 [NR]
1.38 [NR]		 Illumina
[551,642]		 N
01/16/09 " Multiple sclerosis (age of onset) 978 cases, 883 controls NR 11q14.2
7q22.1
8q13.3
18q21.31
9q21.13
1q25.2
5q33.2
2q21.2		 RAB38
RELN
KCNB2
WDR7
RFK
C1orf125
SGCD
FLJ34870		 rs1386330-?
rs17157903-?
rs2116078-?
rs1557351-?
rs2842483-?
rs12047808-?
rs4704970-?
rs1437898-?		 0.13
0.14
0.48
0.22
0.29
0.13
0.20
0.40		 2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[551,642]		 N
01/16/09 " Multiple sclerosis (severity) 794 cases, 883 controls NR 3q25.32
4q28.3
19q13.42
4q13.2
7p21.3
11q23.3
16q22.3
6p23
7q31.2
18q22.3
19p13.2		 FLJ16641
LOC132321
NLRP11
CENPC1
C1GALT1
MGC13125
C16orf47
JARID2
MET
CBLN2
ACP5		 rs12638253-?
rs1478091-?
rs299175-?
rs10518025-?
rs10259085-?
rs180358-?
rs7191888-?
rs6941421-?
rs10243024-?
rs337718-?
rs7253363-?		 0.47
0.06
0.46
0.14
0.46
0.23
0.17
0.24
0.23
0.29
0.05		 2 x 10-6
2 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
9 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[551,642]		 N
01/16/09 " Normalized brain volume 753 cases, 883 controls NR 12p11.21
6q21
10p11.23
10q25.2
5q35.1		 BICD1
FOXO3
SVIL
MXI1
KCNIP1		 rs261902-?
rs9480865-?
rs1927457-?
rs716595-?
rs11957313-?		 0.16
0.16
0.31
0.08
0.13		 4 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR		 Illumina
[551,642]		 N
12/09/08 Aulchenko
November 09, 2008
Nat Genet
Genetic variation in the KIF1B locus influences susceptibility to multiple sclerosis. 		Multiple sclerosis 45 cases, 195 controls 2,634 cases, 2,930 controls 1p36.22 KIF1B rs10492972-C 0.27 3 x 10-10 1.34 [1.23-1.48] Affymetrix
[~250,000]		 N
12/01/08 Bilguvar
November 09, 2008
Nat Genet
Susceptibility loci for intracranial aneurysm in European and Japanese populations. 		Intracranial aneurysm 1,580 European cases, 6,276 European controls 495 Japanese cases, 676 Japanese controls 8q11.23
9q21.3
8q11.23-q12.1
2q33.1		 SOX17
CDKN2A, CDKN2B
SOX17
BOLL, PLCL1		 rs10958409-A
rs1333040-T
rs9298506-A
rs700651-G		 0.15
0.55
0.81
0.35		 1 x 10-10
1 x 10-10
2 x 10-9
4 x 10-8 		1.36 [1.24-1.49]
1.29 [1.19-1.40]
1.35 [1.22-1.49]
1.24 [1.15-1.34]		 Illumina
[289,271]		 N
12/30/08 Drgon
November 09, 2008
Mol Med
Genome wide association for nicotine dependence and smoking cessation success in NIH research volunteers 		Nicotine dependence 220 cases, 260 controls 2,271 cases, 1,868 controls NS NS NS NS NS NS Affymetrix
[~600,00] (pooled)		 N
12/09/08 Pankratz
November 06, 2008
Hum Genet
Genomewide association study for susceptibility genes contributing to familial Parkinson disease. 		Parkinson's disease (familial) 857 cases, 867 controls 262 cases, 260 controls 4p16.3 GAK, DGKQ rs1564282-T 0.09 7 x 10-7 1.7 [NR] Illumina
[328,189]		 N
12/09/08 Cronin
November 05, 2008
Eur J Hum Genet
Screening for replication of genome-wide SNP associations in sporadic ALS. 		Amyotrophic lateral sclerosis 958 cases, 932 controls 309 cases, 404 controls 7q36.2 DPP6 rs10260404-C 0.35 3 x 10-6 1.37 [1.20-1.56] Illumina
[287,522]		 N
12/01/08 Neale
November 03, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association scan of attention deficit hyperactivity disorder 		Attention deficit hyperactivity disorder 909 trios NR NS NS NS NS NS NS Perlegen
[438,784]		 N
11/25/08 Cooper
November 02, 2008
Nat Genet
Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. 		Type 1 diabetes 3,561 cases, 4,646 controls 6,225 cases, 6,946 controls, 3,064 trios 6p21.32
1p13.2
12q24.13
12q13.2
15q25.1
16p13.13
6q15
2q33.2
10p15.1
22q13.1
18p11.21
10p15.1
16p13.13
2p23.3		 HLA
PTPN22
C12orf30
ERBB3
CTSH
CLEC16A
BACH2
CTLA4
PRKCQ
C1QTNF6
PTPN2
IL2RA
C16orf75, PRM3, TNP2
Intergenic		 rs9272346-G
rs6679677-A
rs17696736-G
rs2292239-A
rs3825932-T
rs12708716-G
rs11755527-G
rs3087243-A
rs947474-G
rs229541-T
rs2542151-C
rs12251307-T
rs416603-T
rs2165738-C		 NR
NR
NR
NR
0.68
NR
0.47
NR
0.19
0.43
NR
NR
0.44
0.27		 6 x 10-129
1 x 10-40
6 x 10-18
3 x 10-16
3 x 10-15
7 x 10-13
5 x 10-12
8 x 10-11
4 x 10-9
2 x 10-8
9 x 10-8
2 x 10-6
3 x 10-6
4 x 10-6 		NR
NR
NR
NR
1.16 [1.10-1.22]
NR
1.13 [1.08-1.19]
NR
1.1 [1.03-1.18]
1.11 [1.05-1.16]
NR
NR
1.06 [1.01-1.12]
1.07 [1.01-1.13]		 Affymetrix
[up to 335,565]		 N
12/09/08 McKay
November 02, 2008
Nat Genet
Lung cancer susceptibility locus at 5p15.33. 		Lung cancer 2,971 cases, 3,746 controls 2,899 cases, 5,573 controls 15q25.1
5p15.33		 Intergenic
TERT, CLPTM1L		 rs1051730-A
rs402710-C		 NR
NR		 1 x 10-15
4 x 10-6 		1.35 [1.25-1.45]
1.18 [1.12-1.24]		 Illumina
[315,194]		 N
11/25/08 Wang
November 02, 2008
Nat Genet
Common 5p15.33 and 6p21.33 variants influence lung cancer risk. 		Lung cancer 1,952 cases, 1,438 controls 7,579 cases, 8,236 controls 15q25.1
6p21.33
5p15.33		 NR
BAT3,MSH5
CLPTM1L		 rs8042374-?
rs3117582-C
rs401681-G		 NR
NR
NR		 8 x 10-12
5 x 10-10
8 x 10-9 		NR
1.24 [1.16-1.33]
1.15 [1.09-1.19]		 Illumina
[223,891]		 N
12/09/08 Bertram
October 29, 2008
Am J Hum Genet
Genome-wide association analysis reveals putative Alzheimer's disease susceptibility loci in addition to APOE. 		Alzheimer's disease 941 affected individuals, 404 unaffected individuals 1,767 affected individuals, 838 unaffected individuals 14q31.2
19q13.33		 Intergenic
CD33		 rs11159647-?
rs3826656-?		 NR
NR		 2 x 10-6
6 x 10-6 		NR
NR		 Affymetrix
[484,522]		 N
12/09/08 Anney
October 24, 2008
Am J Med Genet B Neuropsychiatr Genet
Conduct disorder and ADHD: evaluation of conduct problems as a categorical and quantitative trait in the international multicentre ADHD genetics study. 		Attention deficit hyperactivity disorder and conduct disorder 938 affected trios NR 13q33.3
11q21
21q21.1
12q21.2
15q26.2
1q42.13
2p22.3
11q24.2
14q12
7q31.1
8q22.3
16q21
18q21.31
9p24.1
12q15
16q22.3
16q23.2
2p12
1q23.1
2q33.1
5q31.1
10p15.2
13q12.2
16p13.3
1p35.2
1q25.3		 LIG4, ABHD13
AMOTL1, CWC15, JMJD2D
Intergenic
PAWR
SPATA8
LOC729257
Intergenic
KIRREL3
Intergenic
FLJ31818, GPR85
YWHAZ
Intergenic
ATP8B1
PTPRD
C12orf28
PKD1L3, KIAA0174, DHODH
PKD1L2, C16orf46
Intergenic
ETV3L, ETV3
FLJ39061, FZD7
C5orf15
PITRM1
GSX1, PDX1
A2BP1
Intergenic
RGL1, GLT25D2		 rs10492664-C
rs10831284-G
rs2826340-T
rs7297018-A
rs4533251-T
rs701157-C
rs6733379-G
rs1557488-T
rs1951082-T
rs10229603-C
rs931812-C
rs1381102-A
rs7236632-A
rs10815798-A
rs789560-G
rs16973500-C
rs4889240-T
rs7595103-A
rs6427356-G
rs1521882-A
rs1644305-A
rs2764980-A
rs9512900-C
rs12921846-A
rs2180233-C
rs10797919-G		 0.84
0.13
0.17
0.19
0.15
0.45
0.28
0.18
0.43
0.31
0.74
0.40
0.86
0.48
0.87
0.86
0.45
0.64
0.28
0.82
0.41
0.51
0.37
0.40
0.31
0.59		 1 x 10-6
2 x 10-6
2 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
7 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6
9 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Perlegen
[378,332]		 N
12/01/08 Johansson
October 24, 2008
Hum Mol Genet
Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide association analysis. 		Height 3,925 individuals 38,091 individuals 7p15.1 JAZF1 rs1635852-A NR 9 x 10-10 .25 [0.17-0.33] cm taller Illumina
[NR]		 N
12/09/08 Comabella
October 22, 2008
PLoS One
Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms. 		Multiple sclerosis 242 cases, 242 controls 375 cases, 375 controls 6p21.32 HLA-DRB1 rs3129934-T NR 9 x 10-11 3.3 [2.3-4.9] Affymetrix
[428,867] (pooled)		 N
11/25/08 Hillmer
October 12, 2008
Nat Genet
Susceptibility variants for male-pattern baldness on chromosome 20p11. 		Male-pattern baldness 296 cases, 347 controls 319 cases, 234 controls 20p11.22 PAX1, BQ013595, BE789145 rs2180439-C 0.43 3 x 10-15 1.82 [1.45-2.30] Illumina
[531,695]		 N
11/25/08 Richards
October 12, 2008
Nat Genet
Male-pattern baldness susceptibility locus at 20p11. 		Male-pattern baldness 578 cases, 547 controls 1,351 cases, 2,485 controls 20p11.22
Xq12		 PAX1
AR		 rs1160312-A
rs6625163-A		 0.43
NR		 1 x 10-14 (males)
5 x 10-11 		1.6 [1.42-1.80] (males)
3.3 [2.31-4.71]		 Affymetrix
[370,102]		 N
11/25/08 Stacey
October 12, 2008
Nat Genet
Common variants on 1p36 and 1q42 are associated with cutaneous basal cell carcinoma but not with melanoma or pigmentation traits. 		Basal cell carcinoma (cutaneous) 930 cases, 33,117 controls 1,216 cases, 2,844 controls 1p36.13
1q42.13		 PADI4, PADI6,RCC2, ARHGEF10L
RHOU		 rs7538876-A
rs801114-G		 0.35
0.33		 4 x 10-12
6 x 10-12 		1.28 [1.19-1.37]
1.28 [1.19-1.37]		 Illumina
[304,083]		 N
12/01/08 Yuan
October 10, 2008
Am J Hum Genet
Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes. 		Plasma levels of liver enzymes 7,751 European white individuals 4,704 European white and Indian Asian individua 9p34.2
9q34.2
22q13.31
1p36.12
6p22.2
22q11.23
12q24.31
10q21.2
10q21.1
10q24.2
1q24.1		 ABO
ADAMTS13
PNPLA3, SAMM50
NBPF3, ALPL, RAP1GAP
GPLD1
GGT1, C22orf36
HNF1A, C12orf27, C12orf43
JMJD1C
REEP3
CPN1, CHUK, ERLIN1
POU2F1		 rs657152-T
rs4962153-A
rs2281135-T
rs1780324-T
rs9467160-A
rs4820599-G
rs1169313-C
rs12355784-A
rs10761779-G
rs11597390-A
rs9803659-C		 0.39
NR
0.18
0.43
0.24
0.31
0.38
0.48
0.49
0.36
NR		 2 x 10-30 (ALP)
8 x 10-21 (ALP)
8 x 10-16 (ALT)
7 x 10-15 (ALP)
1 x 10-11 (ALP)
4 x 10-11 (GGT)
2 x 10-10 (GGT)
5 x 10-10 (ALP)
7 x 10-10 (ALP)
2 x 10-8 (ALT)
4 x 10-6 (ALT)		 .05 [0.039-0.055] U/L decrease
.06 [0.048-0.072] U/L decrease
.06 [0.046-0.074] U/L increase
.03 [0.023-0.039] U/L increase
.03 [0.024-0.044] U/L increase
.01 [0.005-0.009] U/L increase
.01 [0.003-0.007] U/L decrease
.03 [0.017-0.033] U/L increase
.03 [0.017-0.033] U/L increase
.04 [0.025-0.053] U/L decrease
.03 [0.018-0.042] U/L decrease		 Affymetrix and Illumina
[up to 496,032]		 N
11/25/08 Grant
October 07, 2008
Diabetes
Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. 		Type 1 diabetes 563 cases, 1,146 controls, 483 case-parents trios 636 families, 3,303 cases, 4,673 controls 21q22.3
6q15
1p22.3
9p24.2
15q14		 UBASH3A
BACH2
EDG7
GLIS3
RASGRP1		 rs9976767-C
rs3757247-A
rs1983853-?
rs10758593-A
rs8035957-C		 NR
NR
NR
NR
NR		 2 x 10-8
1 x 10-6
2 x 10-6
3 x 10-6
4 x 10-6 		1.16 [1.10-1.22]
1.13 [1.08-1.19]
1.2 [1.11-1.29]
1.13 [1.07-1.19]
1.14 [1.08-1.21]		 Illumina
[up to 1,000,000]		 N
05/07/09 Lesch
October 07, 2008
J Neural Transm
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. 		Attention deficit hyperactivity disorder 343 cases, 304 controls NR 13q31.3
3p22.1
9q34.13
15q23
17p13.2
9q33.1
2q14.2
1p35.1
15q26.1
16q24.1
15q26.1
10q24.1
5q13.2
9q34.11
6p21.1
10q22.1
10q25.1
20q11.22
12q23.3
6p21.1
7p15.1
22q11.22
16q23.3
2p25.3
2q33.3
5q22.2		 GPC6
MOBP
C9orf98
ITGA11
ITGAE
ASTN2
MGC33657
CSMD2
AK094352
ATP2C2
MAN2A2
TLL2
MAP1B
DNM1
TFEB
UNC5B
C10orf79
MMP24
NT5DC3
SUPT3H
CREB5
PPM1F
CDH13
MYT1L
CRYGC
REEP5		 rs7995215-?
rs864643-?
rs11243897-?
rs7164335-?
rs220470-?
rs10983238-?
rs2587695-?
rs2281597-?
rs7175404-?
rs10514604-?
rs2677744-?
rs10786284-?
rs2199161-?
rs2502731-?
rs2842643-?
rs16928529-?
rs515910-?
rs1555322-?
rs4964805-?
rs3799977-?
rs2237349-?
rs412050-?
rs11646411-?
rs2241685-?
rs2242073-?
rs469727-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-8
1 x 10-8
6 x 10-8
1 x 10-7
1 x 10-7
1 x 10-7
3 x 10-7
5 x 10-7
6 x 10-7
8 x 10-7
1 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[504,219](pooled)		 N
12/09/08 Sonuga-Barke
October 07, 2008
Am J Med Genet B Neuropsychiatr Genet
Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan. 		Attention deficit hyperactivity disorder symptoms (interaction) 909 trios NR 11q21
13q12.3
6p21.2
14q24.3
21q21.1
3q27.2
8p23.2		 PIWIL4
Intergenic
KIF6
Intergenic
Intergenic
Intergenic
Intergenic		 rs2212361-C
rs1161463-C
rs4714261-T
rs2360997-C
rs2825388-A
rs10049246-G
rs4875598-G		 0.26
0.79
0.17
0.86
0.40
0.59
0.34		 9 x 10-7 (int, MW)
2 x 10-6 (int, MW)
2 x 10-6 (int, MW)
8 x 10-6 (int, MW)
8 x 10-6 (int, MC)
8 x 10-6 (int, MW)
9 x 10-6 (int, MW)		 .97 [NR] unit decrease
1.72 [NR] unit decrease
.95 [NR] unit increase
1.3 [NR] unit decrease
1.06 [NR] unit increase
.6 [NR] unit increase
.94 [NR] unit decrease		 Perlegen
[429,981]		 N
12/09/08 " Conduct disorder (interaction) 909 trios NR 5q21.1
16p13.3
4q23
2p21
10q22.3
3p25.3
8p23.1
15q26.2
18q12.3
1q22
4q22.1
17q22
2p22.2
11q23.2
6p15		 Intergenic
A2BP1
ADH1C
Intergenic
Intergenic
SLC6A1
MFHAS1
Intergenic
Intergenic
RIT1
PPM1K
Intergenic
Intergenic
ZBTB16
Intergenic		 rs13188771-A
rs6500744-C
rs1789891-A
rs719593-T
rs2395528-T
rs9990174-T
rs332034-A
rs4321143-G
rs17664267-T
rs2282301-A
rs893971-T
rs8073783-C
rs604381-A
rs17116334-T
rs16880441-G		 0.17
0.53
0.14
0.86
0.23
0.33
0.85
0.28
0.19
0.23
0.60
0.49
0.32
0.16
0.08		 2 x 10-6 (int, MW)
3 x 10-6 (int, MW)
3 x 10-6 (int, MW)
5 x 10-6 (int, MC)
6 x 10-6 (int, MW)
6 x 10-6 (int, MW)
6 x 10-6 (int, MW)
7 x 10-6 (int, MC)
7 x 10-6 (int, MW)
7 x 10-6 (int, MW)
7 x 10-6 (int, MC)
8 x 10-6 (int, MW)
8 x 10-6 (int, MW)
9 x 10-6 (int, MC)
9 x 10-6 (int, MC)		 4.24 [NR] unit decrease
.91 [NR] unit increase
1.47 [NR] unit increase
2.05 [NR] unit decrease
1.46 [NR] unit decrease
2.52 [NR] unit decrease
1.05 [NR] unit increase
1.13 [NR] unit increase
1.39 [NR] unit increase
2.88 [NR] unit increase
1.15 [NR] unit decrease
1.76 [NR] unit decrease
1.26 [NR] unit increase
1.3 [NR] unit increase
1.63 [NR] unit increase		 Perlegen
[429,901)		 N
11/25/08 Franke
October 05, 2008
Nat Genet
Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility. 		Ulcerative colitis 1,167 cases, 777 controls 1,855 cases, 3,091 controls 6p21.32
1q32.1		 HLA-DRA, BTNL2
IL10		 rs9268877-T
rs3024505-T		 0.45
0.15		 6 x 10-18
1 x 10-12 		1.45 [1.33-1.58]
1.46 [1.31-1.62]		 Affymetrix
[355,262]		 N
10/14/09 Chasman
October 01, 2008
Circ Cardiovasc Genet
Genetic loci associated with plasma concentration of LDL-C, HDL-C, triglycerides, ApoA1, and ApoB among 6382 Caucasian women in genome-wide analysis with replication 		Lipid traits 6,382 Caucasian women 970 Caucasian individuals NS NS NS NS NS NS Illumina
[314,518]		 N
11/25/08 Dehghan
October 01, 2008
Lancet
Association of three genetic loci with uric acid concentration and risk of gout: a genome-wide association study. 		Serum urate 11,847 individuals 14,867 individuals 4p16.1
4q22.1
6p22.2		 SLC2A9
ABCG2
SLC17A3		 rs16890979-T
rs2231142-?
rs1165205-?		 0.23
0.11
0.47		 7 x 10-168 (whites)
3 x 10-60 (whites)
4 x 10-29 (whites)		 .34 [0.30-0.38] SD decrease in serum uric acid level
.24 [0.20-0.28] SD increase in serum uric acid level
.09 [0.07-0.11] SD decrease in serum uric acid level		 Affymetrix and Illumina
[up to 530,683]		 N
12/09/08 Gretarsdottir
October 01, 2008
Ann Neurol
Risk variants for atrial fibrillation on chromosome 4q25 associate with ischemic stroke. 		Ischemic stroke 1,661 cases, 10,815 controls 4,576 cases, 19,343 controls 4q25 NR rs2200733-T 0.11 2 x 10-10 1.26 [1.17-1.35] Illumina
[310,881]		 N
01/13/10 Heid
October 01, 2008
Circ Cardiovasc Genet
Genome-wide association analysis of high-density lipoprotein cholesterol in the population-based KORA study sheds new light on intergenic regions. 		HDL cholesterol Up to 4,274 European individuals Up to 15,873 European individuals 16q13
8p21.3
18q21.1		 CETP
LPL
LIPG		 rs9989419-A
rs17482753-T
rs7240405-A		 0.38
0.11
0.15		 9 x 10-27
3 x 10-11
5 x 10-10 		2.66 [NR] mg/dl decrease
2.02 [NR] mg/dl increase
2.27 [NR] mg/dl decrease		 Affymetrix
[up to 2,557,253] (imputed)		 N
11/25/08 Mushiroda
October 01, 2008
J Med Genet
A genome-wide association study identifies an association of a common variant in TERT with susceptibility to idiopathic pulmonary fibrosis. 		Idiopathic pulmonary fibrosis 159 Japanese cases, 934 Japanese controls 83 Japanese cases, 535 Japanese controls 5p15.33 TERT rs2736100-A 0.41 3 x 10-8 2.11 [1.61-2.78] Illumina
[214,508]		 N
11/25/08 Abraham
September 29, 2008
BMC Med Genomics
A genome-wide association study for late-onset Alzheimer's disease using DNA pooling. 		Alzheimer's disease 1,082 cases, 1,239 controls 1,400 additional controls 19q13.32
4q32.1		 PVRL2, TOMM40, APOE
Intergenic		 rs6859-A
rs727153-C		 NR
0.52		 6 x 10-14
3 x 10-6 		NR
1.63 [1.37-1.95]		 Illumina
[561,494] (pooled)		 N
11/25/08 Miyagawa
September 28, 2008
Nat Genet
Variant between CPT1B and CHKB associated with susceptibility to narcolepsy. 		Narcolepsy 222 Japanese cases, 389 Japanese controls 748 cases, 994 controls 22q13.33 CPT1B rs5770917-C 0.17 6 x 10-8 1.63 [1.37-1.95] Affymetrix
[249,133]		 N
11/25/08 Mick
September 26, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome-wide association study of response to methylphenidate in 187 children with attention-deficit/hyperactivity disorder. 		Attention deficit hyperactivity disorder 187 children NR 22q13.31
5p15.31		 Intergenic
Intergenic		 rs9627183-C
rs11134178-T		 0.03
0.05		 3 x 10-6
3 x 10-6 		NR
NR		 Affymetrix
[319,722]		 N
12/09/08 Burkhardt
September 18, 2008
Arterioscler Thromb Vasc Biol
Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. 		LDL cholesterol 2,346 Micronesian individuals 1,464 European white cases, 1,467 European white controls 5q13.3
19q13.32		 HMGCR
APOE, APOC1, APOC4, APOC2		 rs7703051-A
rs4420638-?		 0.41
NR		 1 x 10-8
2 x 10-7 		18 [NR] % s.d. increase
NR		 Affymetrix
[~500,000]		 N
11/25/08 Liu
September 17, 2008
J Natl Cancer Inst
Familial aggregation of common sequence variants on 15q24-25.1 in lung cancer. 		Lung cancer 194 cases, 219 controls 3,878 cases, 4,831 controls 15q25.1 LOC123688, PSMA4, CHRNA3, CHRNA5, CHRNB4 rs8034191-G NR 1 x 10-8 1.38 [1.17-1.64] Affymetrix
[up to 722,376]		 N
11/25/08 Kiemeney
September 14, 2008
Nat Genet
Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. 		Urinary bladder cancer 1,803 cases, 34,336 controls 2,165 cases, 3,800 controls 8q24.21
3q28		 MYC, BC042052
TP63		 rs9642880-T
rs710521-A		 0.45
0.73		 9 x 10-12
1 x 10-7 		1.22 [1.15-1.29]
1.19 [1.12-1.27]		 Illumina
[302,140]		 N
11/25/08 Raychaudhuri
September 14, 2008
Nat Genet
Common variants at CD40 and other loci confer risk of rheumatoid arthritis. 		Rheumatoid arthritis 3,393 cases, 12,460 controls 3,929 cases, 5,807 controls 6p21.32
1p13.2
6q23.3
20q13.12
9p13.3
12q13.3
1p36.32
10p15.1
7q21.2		 HLA-DRB1
PTPN22
OLIG3, TNFIP3
CD40
CCL21
KIF5A,PIP4K2C
MMEL1,TNFRSF14
PRKCQ
CDK6		 rs6457620-?
rs6679677-?
rs6920220-?
rs4810485-G
rs2812378-G
rs1678542-C
rs3890745-T
rs4750316-G
rs42041-G		 0.50
0.10
0.22
0.75
0.34
0.37
0.67
0.20
0.24		 4 x 10-186
6 x 10-42
2 x 10-9
8 x 10-9
3 x 10-8
9 x 10-8
1 x 10-7
4 x 10-6
4 x 10-6 		2.55 [2.40-2.71]
1.79 [1.65-1.94]
1.24 [1.16-1.32]
1.15 [NR]
1.12 [NR]
1.12 [NR]
1.12 [NR]
1.14 [NR]
1.11 [NR]		 Illumina
[818,728] Affymetrix
[~340,000] (imputed)		 N
11/25/08 Huyghe
September 12, 2008
Am J Hum Genet
Genome-wide SNP-based linkage scan identifies a locus on 8q24 for an age-related hearing impairment trait 		Hearing impairment 1,081 individuals NR NS NS NS NS NS NS Affymetrix
[169,154]		 N
11/25/08 Liu
September 08, 2008
PLoS One
Identification of PLCL1 gene for hip bone size variation in females in a genome-wide association study. 		Hip bone size 501 women, 499 men 1,216 women 2q33.1 PLCL1 rs7595412-A 0.89 2 x 10-6 5 [NR] cm2 increase in hip bone size on women Affymetrix
[306,823]		 N
11/25/08 Hazra
September 07, 2008
Nat Genet
Common variants of FUT2 are associated with plasma vitamin B12 levels. 		Plasma level of vitamin B12 1,658 women 1,059 women 19q13.33 FUT2 rs492602-G 0.49 5 x 10-17 .09 [0.07-0.11] pg/ml decrease Illumina
[528,134]		 N
11/25/08 McArdle
September 01, 2008
Arthritis Rheum
Association of a common nonsynonymous variant in GLUT9 with serum uric acid levels in old order amish. 		Serum uric acid 408 women, 460 men NR 4p16.1
13q33.1
2q31.1
13q14.11
3p24.3
20p12.3
5q31.3		 GLUT9, WDR1
NR
NR
NR
NR
NR
NR		 rs16890979-?
rs4771450-?
rs4668338-?
rs17065323-?
rs6442522-?
rs6085920-?
rs3776331-?		 NR
NR
NR
NR
NR
NR
NR		 1 x 10-11
2 x 10-6
3 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
8 x 10-6 		.44 [0.32-0.56] mg/dl decrease in uric serum levels
.23 [NR] mg/dl decrease in uric acid levels
4.29 [NR] mg/dl decrease in uric acid levels
4.29 [NR] mg/dl decrease in uric acid levels
.05 [NR] mg/dl increase in uric acid levels
.4 [NR] mg/dl decrease in uric acid levels
.3 [NR] mg/dl increase in uric acid levels		 Affymetrix
[361,034]		 N
11/25/08 van den Oord
September 01, 2008
Arch Gen Psychiatry
Genomewide association analysis followed by a replication study implicates a novel candidate gene for neuroticism. 		Neuroticism 1,227 individuals 1,880 individuals 14q21.3
8q24.23
7p21.3		 MAMDC1
AK127771
NXPH1		 rs12883384-?
rs2705293-?
rs2349775-?		 NR
NR
NR		 7 x 10-7
6 x 10-6
7 x 10-6 		NR
NR
NR		 Affymetrix
[420,287]		 N
11/25/08 Di Bernardo
August 31, 2008
Nat Genet
A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia. 		Chronic lymphocytic leukemia 505 cases, 1,438 controls 1,024 cases, 1,677 controls 6p25.3
11q24.1
15q23
2q13
2q37.1
19q13.32		 IRF4
GRAMD1B
Intergenic
ACOXL,BCL2L11
SP140, SP110
PRKD2,STRN4		 rs872071-G
rs735665-A
rs7176508-A
rs17483466-G
rs13397985-G
rs11083846-A		 0.54
0.21
0.37
0.20
0.19
0.22		 2 x 10-20
4 x 10-12
5 x 10-12
2 x 10-10
6 x 10-10
4 x 10-9 		1.54 [1.41- 1.69]
1.45 [1.31-1.61]
1.37 [1.26-1.50]
1.39 [1.25-1.53]
1.41 [1.26-1.57]
1.35 [1.22-1.49]		 Illumina
[345,665]		 N
11/25/08 Kugathasan
August 31, 2008
Nat Genet
Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease. 		Inflammatory bowel disease 1,011 cases, 4,250 controls 1,922 cases, 14,124 controls 20q13.33
21q22.2
1p31.3
16q12.1
6p21.32
9q32		 TNFRSF6B
PSMG1
IL23R
NOD2
HLA-DQA1
TNFSF15		 rs2315008-G
rs2836878-?
rs11209026-?
rs5743289-T
rs477515-?
rs6478109-?		 0.69
0.72
0.94
0.17
0.69
0.69		 9 x 10-15
4 x 10-12
7 x 10-11
4 x 10-10
1 x 10-8
3 x 10-8 		1.36 [1.05-1.76]
1.41 [1.08-1.84]
2.56 [1.92-3.45]
1.46 [1.29-1.64]
1.38 [1.23-1.54]
1.36 [1.22-1.52]		 Illumina
[NR]		 N
11/25/08 Galvan
August 26, 2008
Int J Cancer
A polygenic model with common variants may predict lung adenocarcinoma risk in humans 		Lung adenocarcinoma 482 cases, 522 controls NR NS NS NS NS NS NS Illumina
[~318,000] (pooled)		 N
11/25/08 Weidinger
August 22, 2008
PLoS Genet
Genome-wide scan on total serum IgE levels identifies FCER1A as novel susceptibility locus. 		Serum IgE levels 1,530 individuals 9,769 individuals 1q23.2
5q31.1		 FCER1A
RAD50		 rs2251746-C
rs2040704-?		 0.26
0.23		 2 x 10-20
4 x 10-8 		19.2 [NR] % decrease
13.9 [NR] % increase		 Affymetrix
[353,569]		 N
11/25/08 Ferreira
August 17, 2008
Nat Genet
Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder. 		Bipolar disorder 4,387 cases, 6,209 controls NR 10q21.2
12p13.33
15q14
2q11.2
9q33.3
11q14.1
15q14
3p22.3
6q25.2
9p13.3
14q11.2
14q13.1
3p24.3
3p24.3
11q24.2
15q25.1
1p21.2
9q31.3
18p11.32
3p26.2
10q22.3		 ANK3
CACNA1C
C15orf53, RASGRP1
Intergenic
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 rs10994336-T
rs1006737-A
rs12899449-?
rs2314398-?
rs4130590-?
rs12290811-A
rs16966460-G
rs4380451-?
rs17082664-G
rs216345-T
rs12436436-C
rs8015959-T
rs3821396-A
rs11720452-?
rs544368-T
rs2278702-?
rs1948368-?
rs7042161-?
rs7226677-G
rs1601875-?
rs703965-?		 0.05
0.32
0.72
0.69
0.56
0.15
0.10
0.73
0.13
0.37
0.08
0.02
0.11
0.58
0.12
0.83
0.51
0.65
0.12
0.50
0.54		 9 x 10-9
7 x 10-8
4 x 10-7
3 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
7 x 10-6
8 x 10-6 		1.45 [NR]
1.18 [NR]
1.2 [NR]
1.17 [NR]
1.16 [NR]
1.2 [NR]
1.26 [NR]
1.18 [NR]
1.22 [NR]
1.15 [NR]
1.3 [NR]
1.59 [NR]
1.23 [NR]
1.15 [NR]
1.22 [NR]
1.21 [NR]
1.15 [NR]
1.15 [NR]
1.24 [NR]
1.14 [NR]
1.15 [NR]		 Affymetrix
[1,769,948] imputed		 N
04/10/09 Unoki
August 17, 2008
Nat Genet
SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. 		Type 2 diabetes 194 Japanese cases, 1,558 Japanese controls 4,924 cases, 2,618 controls (Japanese), 1433 cases, 1,735 controls (Singaporean), 3,891 cases, 4,888 controls (Danish) 11p15.4
6p22.3
3q27.2		 KCNQ1
CDKAL1
IGF2BP2		 rs2237897-C
rs4712524-G
rs6769511-C		 0.34
0.42
0.32		 1 x 10-16
3 x 10-10
1 x 10-9 		1.33 [1.24-1.41]
1.22 [1.15-1.31]
1.23 [1.15-1.31]		 Affymetrix
[207,097]		 N
04/03/09 Yasuda
August 17, 2008
Nat Genet
Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus. 		Type 2 diabetes 187 Japanese cases, 1,504 Japanese controls 6,552 Asian cases, 6,621 Asian controls, 2,830 cases, 3,740 controls (Swedish) 11p15.5 KCNQ1 rs2237892-C 0.61 2 x 10-42 1.4 [1.34-1.47] Invader
[82,343]		 N
11/25/08 Shlien
August 12, 2008
Proc Natl Acad Sci U S A
Excessive genomic DNA copy number variation in the Li-Fraumeni cancer predisposition syndrome 		TP53 carriage 53 carriers, 70 controls 770 individuals Pending Pending Pending Pending Pending Pending Affymetrix
[3,884 CNVs]		 Y
11/25/08 Hofmann
August 10, 2008
Nat Genet
Genome-wide association study identifies ANXA11 as a new susceptibility locus for sarcoidosis 		Sarcoidosis 499 cases, 490 controls 1,649 cases, 1,832 controls NS NS NS NS NS NS Affymetrix
[375,771]		 N
11/25/08 Graham
August 01, 2008
Nat Genet
Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. 		Systemic lupus erythematosus 431 cases, 2,155 controls 740 trios 6q23.3
2q32.3
8p23.1
16p11.2
10q11.22
17p12
4q28.3
2p16.3		 TNFAIP3
STAT4
BLK
ITGAM
c10orf64
Intergenic
Intergenic
Intergenic		 rs5029939-?
rs3821236-?
rs2618476-?
rs11150610-?
rs11101442-?
rs12949531-?
rs2313132-?
rs17039212-?		 0.03
0.19
0.26
0.42
0.32
0.22
0.12
0.10		 3 x 10-12
8 x 10-11
2 x 10-8
2 x 10-6
3 x 10-6
8 x 10-6
8 x 10-6
9 x 10-6 		2.28 [NR]
1.49 [NR]
1.29 [NR]
NR
NR
NR
NR
NR		 Affymetrix
[313,238]		 N
11/25/08 Julia
August 01, 2008
Arthritis Rheum
Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. 		Rheumatoid arthritis 400 cases, 400 controls 410 cases, 394 controls 6p21.32
18q23		 HLA-DQA1, HLA-DQA2
SALL3		 rs6457617-?
rs2002842-A		 NR
0.49		 1 x 10-9
6 x 10-6 		NR
1.61 [NR]		 Illumina
[299,918]		 N
11/25/08 O'Donovan
July 30, 2008
Nat Genet
Identification of loci associated with schizophrenia by genome-wide association and follow-up. 		Schizophrenia 479 cases, 2,937 controls 6,666 cases, 9,897 controls 2q32.1
11p14.1
16p13.12		 ZNF804A
Intergenic
Intergenic		 rs1344706-T
rs1602565-C
rs7192086-T		 0.59
0.11
0.24		 2 x 10-7
3 x 10-6
6 x 10-6 		1.12 [NR]
1.16 [NR]
1.12 [NR]		 Affymetrix
[362,532]		 N
11/25/08 Schormair
July 27, 2008
Nat Genet
PTPRD (protein tyrosine phosphatase receptor type delta) is associated with restless legs syndrome. 		Restless legs syndrome 628 cases, 1,644 controls 1,835 cases, 3,111 controls 9p23
9p24.1		 PTPRD
PTPRD		 rs4626664-A
rs1975197-T		 0.12
0.16		 6 x 10-10
6 x 10-9 		1.44 [1.31-1.59]
1.31 [1.20-1.44]		 Affymetrix
[208,733]		 N
11/25/08 The SEARCH Collaborative Group
July 23, 2008
N Engl J Med
SLCO1B1 variants and statin-induced myopathy--a genomewide study. 		Response to statin therapy 85 cases, 90 controls 19,856 individuals 12p12.1 SLCO1B1 rs4149056-C 0.13 2 x 10-9 4.5 [2.60-7.70] Illumina
[316,184]		 N
11/25/08 Franke
July 21, 2008
Gastroenterology
Genome-wide association analysis in sarcoidosis and Crohn's disease unravels a common susceptibility locus on 10p12.2. 		Crohn's disease and sarcoidosis (combined) 382 CD cases, 398 SA cases, 394 controls 660 CD cases, 657 SA cases, 1,091 controls 10p12.2 C10orf67 rs1398024-A 0.25 4 x 10-6 1.23 [1.04-1.45] Affymetrix
[83,360]		 N
11/25/08 Liu
July 10, 2008
Mol Med
Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis. 		Response to TNF antagonist treatment 89 cases NR 20q12
6q26
9p21.2
7q21.3
20p11.21
2q24.3
4p15.1
1p22.3		 MAFB
QKI
IFNK
PON1
CST5
LASS6
CENTD1
LMO4		 rs6028945-T
rs10945919-G
rs7046653-A
rs854555-A
rs6138150-T
rs13393173-A
rs437943-G
rs983332-A		 0.12
0.32
0.26
0.34
0.84
0.12
0.33
0.21		 2 x 10-7
3 x 10-7
5 x 10-7
2 x 10-6
3 x 10-6
4 x 10-6
4 x 10-6
5 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[283,348]		 N
11/25/08 Pare
July 04, 2008
PLoS Genet
Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women. 		Soluble ICAM-1 4,570 women 2,008 women 19p13.2
9q34.2
19p13.2
19p13.2		 ICAM1
ABO
ICAM1
ICAM1		 rs1799969-A
rs507666-G
rs5498-A
rs281437-?		 0.12
0.20
0.43
0.30		 4 x 10-47
5 x 10-29
5 x 10-25
3 x 10-10 		28.19 [NR] umol/L decrease
17.73 [NR] umol/L decrease
13.22 [NR] umol/L increase
10.1 [NR] umol/L increase		 Illumina
[336,108]		 N
11/25/08 Bae
July 02, 2008
Biochem Biophys Res Commun
Identification of SNP markers for common CNV regions and association analysis of risk of subarachnoid aneurysmal hemorrhage in Japanese population 		Subarachnoid aneurysmal hemorrhage 203 cases, 294 controls NR Pending Pending Pending Pending Pending Pending Illumina
[317,503]		 Y
11/25/08 Sarasquete
July 01, 2008
Blood
Bisphosphonate-related osteonecrosis of the jaw is associated with polymorphisms of the cytochrome P450 CYP2C8 in multiple myeloma: a genome-wide single nucleotide polymorphism analysis. 		Osteonecrosis of the jaw 21 cases, 64 controls NR 10q23.33 CYP2C8 rs1934951-T 0.12 1 x 10-6 12.75 [3.7-43.5] Affymetrix
[339,972]		 N
11/25/08 Turner
June 30, 2008
Hypertension
Genomic association analysis suggests chromosome 12 locus influencing antihypertensive response to thiazide diuretic 		Response to diuretic therapy 194 blacks, 195 whites NR 12q15 LYZ, YEATS4, FRS2 3-SNP haplotype NR 6 x 10-6 NR Affymetrix
[up to 102,334]		 N
11/25/08 Barrett
June 29, 2008
Nat Genet
Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. 		Crohn's disease 3,230 cases 4,829 controls 1,339 trios, 2,325 cases, 1,809 controls 1p31.3
2q37.1
5p13.1
16q12.1
10q21.2
5q31.1
18p11.21
10q24.2
5q33.1
13q14.11
5q33.3
3p21.31
6q27
17q21.2
1q32.1
6q21
12q12
9q32
6p22.3
1q23.3
11q13.5
21q22.3
10p11.21
1q24.3
9p24.1
17q12
7p12.2
8q24.13
21q21.1
1p13.2		 IL23R
ATG16L1
PTGER4
NOD2
ZNF365
Intergenic
PTPN2
NKX2-3
IRGM
Unknown
IL12B
MST1
CCR6
STAT3
Intergenic
Unknown
LRRK2, MUC19
TNFSF15
CDKAL1
ITLN1
C11orf30
ICOSLG
Intergenic
Intergenic
JAK2
ORMDL3
Intergenic
Intergenic
Intergenic
PTPN22		 rs11465804-T
rs3828309-G
rs4613763-C
rs2066847-C
rs10995271-C
rs2188962-T
rs2542151-G
rs11190140-T
rs11747270-G
rs3764147-G
rs10045431-C
rs3197999-A
rs2301436-T
rs744166-A
rs11584383-T
rs7746082-C
rs11175593-T
rs4263839-G
rs6908425-C
rs2274910-C
rs7927894-T
rs762421-G
rs17582416-G
rs9286879-G
rs10758669-C
rs2872507-A
rs1456893-A
rs1551398-A
rs1736135-T
rs2476601-G		 0.93
0.53
0.13
0.02
0.39
0.43
0.15
0.48
0.09
0.22
0.71
0.27
0.46
0.57
0.70
0.29
0.02
0.68
0.78
0.68
0.39
0.39
0.35
0.24
0.35
0.47
0.68
0.62
0.57
0.90		 7 x 10-63
2 x 10-32
7 x 10-27
3 x 10-24
4 x 10-20
2 x 10-18
5 x 10-17
3 x 10-16
3 x 10-16
2 x 10-13
4 x 10-13
1 x 10-12
1 x 10-12
7 x 10-12
1 x 10-11
2 x 10-10
3 x 10-10
3 x 10-10
9 x 10-10
1 x 10-9
1 x 10-9
1 x 10-9
2 x 10-9
2 x 10-9
3 x 10-9
5 x 10-9
5 x 10-9
5 x 10-9
7 x 10-9
1 x 10-8 		2.5 [NR]
1.25 [NR]
1.32 [NR]
3.99 [NR]
1.25 [NR]
1.25 [NR]
1.35 [NR]
1.2 [NR]
1.33 [NR]
1.25 [NR]
1.11 [NR]
1.2 [NR]
1.21 [NR]
1.18 [NR]
1.18 [NR]
1.17 [NR]
1.54 [NR]
1.22 [NR]
1.21 [NR]
1.14 [NR]
1.16 [NR]
1.13 [NR]
1.16 [NR]
1.19 [NR]
1.12 [NR]
1.12 [NR]
1.2 [NR]
1.08 [NR]
1.18 [NR]
1.31 [NR]		 Affymetrix and Illumina
[635,547] (imputed)		 N
11/25/08 Behrens
June 24, 2008
Arthritis Rheum
Association of the TRAF1-C5 locus on chromosome 9 with juvenile idiopathic arthritis. 		Arthritis (juvenile idiopathic) 130 cases 1,952 controls NR 6p21.32 HLA-DRB1 rs2395148-? NR 2 x 10-10 5.37 [3.02-9.56] Illumina
[524,684]		 N
11/25/08 Bouatia-Naji
June 19, 2008
Science
A polymorphism within the G6PC2 gene is associated with fasting plasma glucose levels. 		Fasting plasma glucose 654 normoglycemic individuals 9,353 individuals 2q24.3 G6PC2 rs560887-A 0.30 4 x 10-23 .06 [0.05-0.08] mmol/l decrease Illumina
[392,935]		 N
11/25/08 Cooper
June 05, 2008
Blood
A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. 		Warfarin maintenance dose 181 individuals 374 individuals 16p11.2
10q23.33
12p13.33		 VKORC1
CYP2C9
CACNA1C		 rs10871454-?
rs4086116-?
rs216013-?		 NR
NR
NR		 5 x 10-34
6 x 10-12
9 x 10-7 		NR
NR
NR		 Illumina
[538,629]		 N
11/25/08 Chen
June 04, 2008
J Clin Invest
Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels. 		Fasting plasma glucose 5,088 nondiabetic individuals 18,436 nondiabetic individuals 2q24.3 G6PC2,ABCB11 rs563694-C 0.34 4 x 10-7 NR Illumina
[315,635]		 N
11/25/08 Uhl
June 04, 2008
Arch Gen Psychiatry
Molecular genetics of successful smoking cessation: convergent genome-wide association study results 		Smoking cessation 241 cases, 309 controls NR NS NS NS NS NS NS Affymetrix
[~500,000] (pooled)		 N
11/25/08 Lavedan
June 03, 2008
Mol Psychiatry
Association of the NPAS3gene and five other loci with response of the antipsychotic iloperidone identified in a whole genome association study 		Response to iloperidone treatment (PANSS-T score) 106 individuals 104 individuals NS NS NS NS NS NS Affymetrix
[334,563]		 N
11/25/08 Volpi
June 03, 2008
Mol Psychiatry
Whole genome association study identifies polymorphisms associated with QT prolongation during iloperidone treatment of schizophrenia. 		Response to iloperidone treatment (QT prolongation) 183 individuals NR 10q23.1
14q12
15q26.1
18q12.2
2q31.3
4q32.3		 NRG3
NUBPL
SLCO3A1
BRUNOL4
CERKL
PALLD		 rs4933824-T
rs7142881-A
rs3924426-T
rs4799915-T
rs993648-T
rs17054392-C		 NR
NR
NR
NR
NR
NR		 2 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
3 x 10-6 		NR
NR
NR
NR
NR
NR		 Affymetrix
[339,272]		 N
11/25/08 Brown
May 18, 2008
Nat Genet
Common sequence variants on 20q11.22 confer melanoma susceptibility. 		Melanoma 864 cases, 864 controls 1,230 cases, 1,251 controls 20q11.22 CDC91L1 rs910873-T 0.09 1 x 10-15 1.75 [1.53-2.01] Illumina
[535,150] (pooled)		 N
11/25/08 Sulem
May 18, 2008
Nat Genet
Two newly identified genetic determinants of pigmentation in Europeans 		Burning and freckling 5,130 individuals 3,330 individuals 20q11.22 ASIP rs1015362-G + rs4911414-T 0.08 6 x 10-37 2.56 [2.06-3.18] Illumina
[316,515]		 N
11/25/08 " Freckles 5,130 individuals 3,330 individuals 20q11.22 ASIP rs1015362-G + rs4911414-T 0.08 8 x 10-29 1.95 [1.65-2.32] Illumina
[316,515]		 N
11/25/08 " Red vs. non-red hair color 5,130 individuals 3,330 individuals 20q11.22 ASIP rs1015362-G + rs4911414-T 0.08 3 x 10-9 1.76 [1.34-2.31] Illumina
[316,515]		 N
11/25/08 " Skin sensitivity to sun 5,130 individuals 3,330 individuals 20q11.22 ASIP rs1015362-G + rs4911414-T 0.08 2 x 10-24 1.76 [1.49-2.08] Illumina
[316,515]		 N
11/25/08 Sulem
May 18, 2008
Nat Genet
Two newly identified genetic determinants of pigmentation in Europeans. 		Blond vs. brown hair color 5,130 individuals 3,330 individuals 11q13.2 TPCN2 rs35264875-T 0.22 4 x 10-30 2.49 [1.96-3.15] Illumina
[316,515]		 N
11/25/08 " Blue vs. green eyes 5,130 individuals 3,330 individuals 9p23 TYRP1 rs1408799-C 0.75 6 x 10-17 1.4 [1.25-1.57] Illumina
[316,515]		 N
11/25/08 Han
May 16, 2008
PLoS Genet
A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. 		Black vs. blond hair color 2,287 women up to 8,465 individuals 6p25.3
15q13.1
15q13.1
14q32.12
5p13.3
15q13.1
6p25.3		 IRF4
HERC2
OCA2
SLC24A4
MATP
Intergenic
EXOC2		 rs12203592-T
rs12913832-A
rs11855019-G
rs12896399-G
rs28777-C
rs8033165-T
rs6918152-A		 NR
NR
NR
NR
NR
NR
NR		 7 x 10-127
4 x 10-103
2 x 10-24
8 x 10-21
1 x 10-17
5 x 10-11
6 x 10-8 		.35 [0.33-0.37] decrease in hair color score
.44 [0.40-0.48] decrease in hair color score
.28 [0.22-0.34] decrease in hair color score
.18 [0.14-0.22] increase in hair color score
.46 [0.36-0.56] decrease in hair color score
.12 [0.08-0.16] increase in hair color score
.11 [0.07-0.15] increase in hair color score		 Illumina
[528,173]		 N
11/25/08 " Black vs. red hair color 2,287 women up to 8,465 individuals 15q13.1
6p25.3
16q24.3
15q13.1
5p13.3
15q13.1
6p25.3		 HERC2
IRF4
MC1R
OCA2
MATP
Intergenic
EXOC2		 rs12913832-A
rs12203592-T
rs258322-T
rs11855019-G
rs28777-C
rs8033165-T
rs6918152-A		 NR
NR
NR
NR
NR
NR
NR		 1 x 10-77
9 x 10-28
2 x 10-23
6 x 10-20
9 x 10-14
2 x 10-12
5 x 10-7 		.44 [0.40-0.48] decrease in hair color score
.31 [0.25-0.36] decrease in hair color score
.36 [0.28-0.44] increase in hair color score
.29 [0.23-0.35] decrease in hair color score
.46 [0.34-0.58] decrease in hair color score
.15 [0.11-0.19] increase in hair color score
.11 [0.07-0.15] increase in hair color score		 Illumina
[528,173]		 N
11/25/08 Maris
May 09, 2008
N Engl J Med
Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. 		Neuroblastoma 1,032 cases, 2,043 controls 720 cases, 2,128 controls 6p22.3 FLJ22536, FLJ44180 rs6939340-G 0.50 9 x 10-15 1.37 [1.27-1.49] Illumina
[464,934]		 N
11/25/08 Melzer
May 09, 2008
PLoS Genet
A genome-wide association study identifies protein quantitative trait loci (pQTLs). 		Protein quantitative trait loci 1,200 individuals NR 1q21.3
9q34.2
17q12
11q23.1
12q12
6q26
11q23.3
17p12
12q24.11
13q12.11
18q11.2
1q21.1
22q11.23
17p13.1
6q11.1
19p13.2
17q25.3
15q15.2
16q23.2
2p12
12p12.3
1q21.1
8q21.11
9q31.2
11q24.2
12q24.33
2p13.3
5q35.1
6q23.2
6q24.3
7p21.3
11p15.5
6q22.31
1p21.1
10p11.21
15q21.1
18q12.1
9q22.2
2q23.1
3p12.3
6p21.33
13q12.12
10p12.33
1q23.2
2p15
8q24.21
2p11.2
2q13
11q14.1		 IL6R
ABO
CCL4L2
IL18
PDZRN4,CNTN1
LPA
PAFAH1B2
HS3ST3B1
ATP2A2
FGF3
OSBPL1A
CHD1L
GGT1
SHBG
KHDRBS2
ANGPTL6
C17orf62
CDAN1
BCM01
CTNNA2
EPS8
CHD1L
GDAP1,PI15
TMEM38B
KIRREL3
GPR133
DYSF
DOCK2
EYA4
SASH1
NXPH1
KCNQ1
GJA1
COL11A1
FZD8,ANKRD30A
DUT
DSC3
GADD45G,DIRAS2
EPC2
ROBO1
HLA-C
SACS
CACNB2
CRP
LOC51057
FAM49B
SH2D6
IL1RN
DLG2		 rs4129267-?
rs505922-?
rs4796217-?
rs2250417-?
rs1880887-?
rs7770628-?
rs7112513-?
rs3848445-?
rs11065611-?
rs17369571-?
rs9635963-?
rs4950322-?
rs5751901-?
rs6761-?
rs6455128-?
rs8109578-?
rs9303029-?
rs16957063-?
rs4889294-?
rs11695685-?
rs17415853-?
rs4950322-?
rs6472866-?
rs4742971-?
rs1939992-?
rs10466868-?
rs2900976-?
rs169082-?
rs9402515-?
rs6930337-?
rs1285407-?
rs2237878-?
rs4541776-?
rs10874639-?
rs1779876-?
rs11637235-?
rs2729409-?
rs2081670-?
rs10191411-?
rs9834373-?
rs9461688-?
rs4770433-?
rs7076247-?
rs12093699-?
rs11683229-?
rs10092658-?
rs7577642-?
rs6761276-?
rs3885683-?		 0.37
0.34
0.34
0.44
0.03
0.49
0.13
0.05
0.06
0.16
0.18
0.21
0.39
0.31
0.19
0.08
0.08
0.01
0.47
0.30
0.02
0.21
0.42
0.11
0.26
0.12
0.30
0.48
0.09
0.06
0.35
0.07
0.33
0.12
0.10
0.28
0.26
0.15
0.32
0.17
0.31
0.40
0.37
0.29
0.15
0.07
0.27
0.37
0.11		 2 x 10-57 (sIL-6R)
7 x 10-40 (TNFA)
4 x 10-21 (MIPb)
7 x 10-13 (IL18)
1 x 10-10 (Alkaline phosphatase)
4 x 10-10 (LPA)
6 x 10-9 (Soluble transferrin receptor)
8 x 10-9 (Ft3)
1 x 10-7 (Alpha-1 globulin)
1 x 10-7 (IL1RA)
2 x 10-7 (SHBG)
2 x 10-7 (Resistin)
2 x 10-7 (GGT1)
3 x 10-7 (SHBG)
3 x 10-7 (GOT (AST))
4 x 10-7 (TSH)
4 x 10-7 (Free IGF1)
5 x 10-7 (Ft4)
5 x 10-7 (IL1B)
5 x 10-7 (IL10)
7 x 10-7 (Ferritin)
7 x 10-7 (Hgb)
8 x 10-7 (myoglobin)
8 x 10-7 (GPT (ALT))
1 x 10-6 (Total IGF-1)
1 x 10-6 (Erythropoeitin)
1 x 10-6 (Albumin)
1 x 10-6 (Leptin)
1 x 10-6 (Alpha-2 macroglobulin)
1 x 10-6 (insulin)
1 x 10-6 (TGF-b1)
1 x 10-6 (Lactic dehydrogenase)
2 x 10-6 (GGT)
3 x 10-6 (Fibrinogen)
3 x 10-6 (Lipoprotein A)
3 x 10-6 (Adiponectin)
3 x 10-6 (Parathyroid hormone)
3 x 10-6 (MIP-1b)
4 x 10-6 (IL8)
4 x 10-6 (GP130)
4 x 10-6 (IL18)
4 x 10-6 (IL12)
6 x 10-6 (CRP)
6 x 10-6 (CRP)
6 x 10-6 (IL6)
6 x 10-6 (Aldolase)
7 x 10-6 (sIL-6R)
7 x 10-6 (IL1RA)
8 x 10-6 (MCP1)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Illumina
[496,032]		 N
11/25/08 Kibriya
May 08, 2008
Breast Cancer Res Treat
A pilot genome-wide association study of early-onset breast cancer. 		Breast cancer 30 cases, 30 controls NR 16q22.3 GLG1 3-SNP haplotype 1 0.34 4 x 10-7 NR Affymetrix
[200,220]		 N
11/25/08 Valdes
May 08, 2008
Am J Hum Genet
Genome-wide association scan identifies a prostaglandin-endoperoxide synthase 2 variant involved in risk of knee osteoarthritis. 		Knee osteoarthritis 357 cases, 285 controls 1,177 cases, 2,372 controls 1q31.1
2q33.3		 PTGS2, PLA2G4A
PARD3B		 rs4140564-?
rs1207421-?		 0.05
0.09		 3 x 10-6
6 x 10-6 		1.59 [1.31-1.94]
1.46 [1.24-1.73]		 Illumina
[413,461]		 N
11/25/08 Chambers
May 04, 2008
Nat Genet
Common genetic variation near MC4R is associated with waist circumference and insulin resistance. 		Waist circumference and related phenotypes 2,684 Asian Indian men 11,955 Asian Indian and European individuals 16q13
18q21.32
2p23.3
8p21.3		 CETP
MC4R
GCKR
LPL		 rs3764261-?
rs12970134-A
rs1260326-?
rs2083637-?		 NR
0.36
NR
NR		 1 x 10-27 (HDL cholesterol)
2 x 10-9 (waist circumference)
4 x 10-8 (triglycerides)
5 x 10-6 (HDL cholesterol)		 NR
.88 [0.59-1.17] cm increase
NR
NR		 Illumina
[308,067]		 N
11/25/08 Loos
May 04, 2008
Nat Genet
Common variants near MC4R are associated with fat mass, weight and risk of obesity. 		Body mass index 16,876 individuals 60,352 individuals 18q21.32
16q12.2		 MC4R
FTO		 rs17782313-C
rs1121980-?		 0.24
NR		 3 x 10-15
4 x 10-8 		.05 [0.04-0.06] unit increase in log(BMI)
.06 [0.04-0.08] unit increase in log(BMI)		 Affymetrix
[344,883]		 N
11/25/08 Poduslo
April 30, 2008
Am J Med Genet B Neuropsychiatr Genet
Genome Screen of Late-Onset Alzheimer's Extended Pedigrees Identifies TRPC4AP by Haplotype Analysis 		Alzheimer's disease 29 siblings from 2 affected families, 60 unrelated controls 199 patients, 85 spouses NS NS NS NS NS NS Affymetrix
[469,218]		 N
11/25/08 Richards
April 29, 2008
Lancet
Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study. 		Bone mineral density 2,094 women 6,463 individuals 11q13.2
8q24.12		 LRP5
TNFRSF11B		 rs3736228-T
rs4355801-A		 0.14
0.53		 6 x 10-12
8 x 10-10 		.13 [NR] SD decrease
.09 [NR] SD decrease		 Illumina
[314,075]		 N
11/25/08 Styrkarsdottir
April 29, 2008
N Engl J Med
Multiple genetic loci for bone mineral density and fractures. 		Bone mineral density (hip) 5,861 individuals 7,925 individuals 1p36.12
8q24.12
6q25.1
13q14.11
6q25.1
18q21.33		 ZBTB40
OPG
ESR1
RANKL
ESR1, C6orf97
RANK		 rs7524102-A
rs6993813-C
rs1038304-G
rs9594738-T
rs4870044-T
rs3018362-A		 0.82
0.50
0.47
0.56
0.28
0.35		 5 x 10-16
3 x 10-11
5 x 10-9
2 x 10-8
2 x 10-7
1 x 10-6 		.15 [0.11-0.19] s.d. decrease
.09 [0.07-0.12] s.d. decrease
.08 [0.06-0.11] s.d. decrease
.1 [0.06-0.13] s.d. decrease
.08 [0.05-0.11] s.d. decrease
.07 [0.04-0.10] s.d. decrease		 Illumina
[301,019]		 N
11/25/08 " Bone mineral density (spine) 5,861 individuals 7,925 individuals 13q14.11
8q24.12
6p25.1
6q25.1
1p36.12
6q25.1
6p21.32
2p16.2		 RANKL
OPG
ESR1
ESR1, C6orf97
ZBTB40
ESR1, C6orf97
MHC, C6orf10
SPTBN1		 rs9594759-T
rs6469804-A
rs4870044-T
rs1038304-G
rs7524102-A
rs1999805-C
rs3130340-T
rs11898505-G		 0.62
0.51
0.28
0.47
0.82
0.44
0.79
0.67		 2 x 10-21
7 x 10-15
2 x 10-11
4 x 10-11
9 x 10-9
2 x 10-8
1 x 10-7
8 x 10-7 		.17 [0.14-0.21] s.d. decrease
.12 [0.09-0.15] s.d. decrease
.11 [0.08-0.14] s.d. decrease
.1 [0.07-0.13] s.d. decrease
.11 [0.07-0.15] s.d. decrease
.09 [0.06-0.12] s.d. decrease
.1 [0.06-0.13] s.d. decrease
.08 [0.05-0.11] s.d. decrease		 Illumina
[301,019]		 N
11/25/08 Walsh
April 25, 2008
Science
Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia 		Schizophrenia 150 cases, 268 controls 83 children, 154 parents Pending Pending Pending Pending Pending Pending Illumina
[~550,000]		 Y
11/25/08 Reiner
April 24, 2008
Am J Hum Genet
Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein. 		C-reactive protein 909 individuals 5,106 individuals 12q24.31
19q13.32
1q23.2		 HNF1A
APOE
CRP		 rs1169310-A
rs2075650-?
rs11265260-?		 0.38
NR
NR		 2 x 10-8
1 x 10-7
7 x 10-6 		.13 [0.08-0.17] mg/l decrease in log(CRP) level
NR
NR		 Illumina
[317,000]		 N
11/25/08 Ridker
April 24, 2008
Am J Hum Genet
Loci related to metabolic-syndrome pathways including LEPR,HNF1A, IL6R, and GCKR associate with plasma C-reactive protein: the Women's Genome Health Study. 		C-reactive protein 6,345 women NR 1q23.2
1p31.3
19q13.32
12q24.31
2p23.3
12q23.2
1q21.3		 CRP
LEPR
APOE
HNF1A
GCKR
Unknown
IL6R		 rs3091244-?
rs1892534-A
rs769449-?
rs7310409-A
rs780094-A
rs10778213-G
rs8192284-?		 NR
NR
NR
NR
NR
NR
NR		 6 x 10-28
7 x 10-21
9 x 10-21
7 x 10-17
7 x 10-15
1 x 10-10
2 x 10-8 		.2 [NR] mg/dl increase
.17 [NR] mg/dl decrease
.26 [NR] mg/dl decrease
.15 [NR] mg/dl decrease
.14 [NR] mg/dl increase
.12 [NR] mg/dl decrease
.1 [NR] mg/dl decrease		 Illumina
[336,108]		 N
11/25/08 Ober
April 09, 2008
N Engl J Med
Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function. 		YKL-40 levels 632 individuals 206 children 1q32.1 CHI3L1 rs4950928-G 0.29 1 x 10-13 .3 [NR] ng/ml decrease Affymetrix
[290,325]		 N
11/25/08 Gudbjartsson
April 06, 2008
Nat Genet
Many sequence variants affecting diversity of adult human height. 		Height 30,968 individuals 8,541 individuals 3q23
12q14.3
7p22.2
6q24.1
4q31.22
6p24.3
2p16.1
14q32.12
1q21.2
4p15.32
6p22.1
17q11.2
18q11.2
1q25.3
6p21.31
7q21.2
20p12.3
9q31.2
15q26.3
1q24.3
6p21.32
6p21.31
8q21.11
17q23.2
8q12.1
17q22
12q22
9q32
6q22.32
17q23.3
6p22.3
16q24.1
20q11.22
2p23.3
6q21
15q25.2
9q22.1
19p13.2
2q35
2q37.1
12p12.2
12p13.2
4q21.21
12q15
Xq21.1
6q21
22q11.23
6q22.33-6q23.1
3q26.2
13q14.3
5q31.1
6p12.3		 ZBTB38
HMGA2
GNA12
GPR126
HHIP
BMP6
EFEMP1, PNPT1
TRIP11, FBLN5, ATXN3, CPSF2
Histone class 2A,MTMR11, SV2A, SF3B4
LCORL, NCAPG
Histone class 1,Butyrophilin genes
CRLF3, ATAD5, CENTA2, RNF135
CABLES1, RBBP8, C18orf45
C1orf19,GLT25D2
HMGA1, LBH
CDK6, PEX1, GATAD1, ERVWE1
BMP2
ZNF462
ADAMTS17
DNM3
HLA class III
ANKS1A, TCP11, ZNF76, DEF6,SCUBE3
PXMP3, ZFHX4
BCAS3, NACA2, TBX2, TBX4
PLAG1, MOS, CHCHD7,RDHE2, RPS20,LYN, TGS1, PENK
NOG, DGKE, TRIM25, COIL, RISK
SOCS2, MRPL42, CRADD, UBE2N
COL27A1
C6orf173
MAP3K3, WDR68, LYK5, MT1F
NUP153, CAP2, KIF13A
ZDHHC7, CRISPLD2, USP10
UQCC, GDF5, CEP250, EIF6, MMP24
ADCY3, RBJ, POMC, DNMT3A, DTNB
LIN28B, HACE1, BVES, POPDC3
ADAMTSL3, SH3GL3
SPIN1, CCRK
ADAMTS10, MYO1F, PRAM1, OR2Z1
IHH, CRYBA2, FEV, SLC23A3, TUBA1
NPPC, DIS3L2, COPS7B, PDE6D, PTMA
PDE3A, SLCO1C1, SLCO1B3
ETV6
BMP3, PRKG2, RASGEF1B
LYZ,YEATS4,FRS2,CPSF6,CCT2,LRRC10
ITM2A
PPIL6, CD164, SMPD2,MNICAL1,ZBTB24
BCR, GNAZ, RTDR1, IGLL1
L3MBTL3, SAMD3
GOLIM4, SERPINI1
DLEU7
PITX1, PCBD2, CATSPER3, TXNDC15,DDX46, CAMLG
SUPT3H, RUNX2		 rs6763931-A
rs8756-C
rs798544-G
rs3748069-A
rs1812175-C
rs12198986-A
rs3791679-T
rs7153027-A
rs11205277-G
rs6830062-T
rs10946808-A
rs3760318-C
rs4800148-A
rs2274432-T
rs1776897-C
rs2282978-C
rs967417-C
rs4743034-A
rs4533267-A
rs678962-G
rs185819-T
rs4713858-G
rs7846385-C
rs757608-T
rs10958476-C
rs4794665-A
rs3825199-C
rs946053-T
rs1490388-T
rs7209435-C
rs12199222-T
rs2326458-C
rs6088792-T
rs6733301-G
rs314268-C
rs2554380-T
rs2814828-T
rs7249094-G
rs1052483-C
rs749052-A
rs11611208-A
rs2187642-A
rs710841-A
rs11177669-A
rs1474563-T
rs9487094-G
rs5751614-A
rs6899976-G
rs4345115-T
rs1239947-G
rs31198-T
rs9395066-C		 0.45
0.52
0.72
0.74
0.86
0.50
0.81
0.52
0.44
0.89
0.70
0.63
0.79
0.37
0.07
0.29
0.53
0.23
0.28
0.22
0.52
0.86
0.27
0.35
0.23
0.48
0.24
0.52
0.42
0.27
0.33
0.26
0.26
0.87
0.34
0.78
0.25
0.59
0.91
0.94
0.06
0.39
0.27
0.31
0.58
0.69
0.49
0.28
0.63
0.35
0.75
0.48		 1 x 10-27
2 x 10-16
7 x 10-15
5 x 10-14
1 x 10-11
2 x 10-11
6 x 10-11
1 x 10-10
1 x 10-10
1 x 10-10
6 x 10-10
2 x 10-9
4 x 10-9
8 x 10-9
1 x 10-8
1 x 10-8
2 x 10-8
2 x 10-8
3 x 10-8
3 x 10-8
3 x 10-8
4 x 10-8
5 x 10-8
6 x 10-8
7 x 10-8
1 x 10-7
2 x 10-7
2 x 10-7
6 x 10-7
7 x 10-7
7 x 10-7
8 x 10-7
8 x 10-7
8 x 10-7
8 x 10-7
9 x 10-7
9 x 10-7
1 x 10-6
1 x 10-6
1 x 10-6
2 x 10-6
2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
4 x 10-6
6 x 10-6
6 x 10-6
7 x 10-6
8 x 10-6
8 x 10-6
8 x 10-6 		7.4 [6.03-8.77] % s.d. taller
6.6 [5.03-8.17] % s.d. taller
5.9 [6.03-8.77] % s.d. taller
6.5 [5.44-9.36] % s.d. taller
8.3 [5.95-10.65] % s.d. taller
6.8 [4.84-8.76] % s.d. taller
5.8 [4.04-7.56] % s.d. taller
5.7 [3.94-7.46] % s.d. taller
5.1 [3.53-6.67] % s.d. taller
6.3 [4.34-8.26] % s.d. taller
5.6 [3.84-7.36] % s.d. taller
6 [4.04-7.96] % s.d. taller
6.4 [4.24-8.56] % s.d. taller
5.3 [3.54-7.06] % s.d. taller
8.8 [5.66-11.94] % s.d. taller
5.8 [3.84-7.76] % s.d. taller
4.3 [2.73-5.87] % s.d. taller
5.3 [3.54-7.06] % s.d. taller
5.6 [3.64-7.56] % s.d. taller
5.4 [3.44-7.36] % s.d. taller
5.2 [3.44-6.96] % s.d. taller
6.8 [4.45-9.15] % s.d. taller
5 [3.24-6.76] % s.d. taller
4.4 [2.83-5.97] % s.d. taller
5.4 [3.44-7.36] % s.d. taller
3.6 [2.23-4.97] % s.d. taller
6.2 [3.85-8.55] % s.d. taller
4.4 [2.83-5.97] % s.d. taller
4.8 [2.84-6.76] % s.d. taller
4.8 [2.84-6.76] % s.d. taller
4.4 [2.64-6.16] % s.d. taller
5.1 [3.14-7.06] % s.d. taller
4.7 [2.74-6.66] % s.d. taller
7.5 [4.56-10.44] % s.d. taller
4.6 [2.84-6.36] % s.d. taller
4.5 [2.74-6.26] % s.d. taller
5.4 [3.24-7.56] % s.d. taller
4.3 [2.54-6.06] % s.d. taller
6.9 [4.16-9.64] % s.d. taller
8.7 [5.17-12.23] % s.d. taller
11.4 [6.7-16.1] % s.d. taller
4.6 [2.64-6.56] % s.d. taller
5 [3.04-6.96] % s.d. taller
4.5 [2.54-6.46] % s.d. taller
3.5 [1.93-5.07] % s.d. taller
4.7 [2.74-6.66] % s.d. taller
4.3 [2.34-6.26] % s.d. taller
3.8 [2.23-5.37] % s.d. taller
4.4 [2.44-6.36] % s.d. taller
3.8 [2.23-5.37] % s.d. taller
4.8 [2.64-6.96] % s.d. taller
3.5 [1.93-5.07] % s.d. taller		 Illumina and Affymetrix
[up to 304,226]		 N
11/25/08 Lettre
April 06, 2008
Nat Genet
Identification of ten loci associated with height highlights new biological pathways in human growth. 		Height 15,821 individuals 13,671 individuals 3q23
12q14.3
6q24.3
6p22.1
20q11.22
4q31.22
14q32.12
6q21
19p13.3
15q25.2
7q36.3
7q21.2
8q12.1
9q34.11
9q33.1
17q22
16p13.3
14q13.3		 ZBTB38
HMGA2
GPR126
HIST1H1D
GDF5,UQCC
HHIP
TRIP11,ATXN3
LIN28B
DOT1L
SH3GL3,ADAMTSL3
WDR60
CDK6
CHCHD7,RDHE2
FUBP3
PAPPA
ANKFN1
RAB40C
NKX2-1		 rs724016-G
rs1042725-T
rs4896582-A
rs10946808-G
rs6060369-C
rs1492820-G
rs8007661-T
rs314277-A
rs12986413-T
rs2562784-G
rs2730245-G
rs2040494-C
rs9650315-T
rs7466269-G
rs7869550-G
rs12449568-C
rs763014-C
rs17104630-G		 0.48
0.49
0.27
0.28
0.36
0.48
0.30
0.13
0.45
0.17
0.33
0.50
0.13
0.33
0.24
0.47
0.43
0.04		 8 x 10-22
3 x 10-20
2 x 10-18
4 x 10-17
1 x 10-16
1 x 10-11
6 x 10-10
1 x 10-8
3 x 10-8
6 x 10-8
3 x 10-7
4 x 10-7
4 x 10-7
8 x 10-7
1 x 10-6
2 x 10-6
5 x 10-6
8 x 10-6 		.37 [0.29-0.45] cm taller
.48 [0.58-1.09] cm shorter
.38 [0.28-0.48] cm shorter
.36 [0.26-0.46] cm shorter
.44 [0.34-0.72] cm taller
.29 [0.21-0.37] cm shorter
.42 [0.30-0.54] cm shorter
.41 [0.26-0.59] cm taller
.31 [0.21-0.46] cm taller
.34 [0.21-0.48] cm taller
.32 [0.19-0.44] cm taller
.26 [0.36-0.65] cm shorter
.43 [0.59-1.07] cm shorter
.27 [0.38-0.69] cm shorter
.33 [0.45-0.82] cm shorter
.25 [0.15-0.35] cm taller
.24 [0.12-0.29] cm taller
.42 [0.61-1.10] cm shorter		 Affymetrix and Illumina
[2,260,683] (imputed)		 N
11/25/08 Weedon
April 06, 2008
Nat Genet
Genome-wide association analysis identifies 20 loci that influence adult height. 		Height 13,665 individuals 16,482 individuals 3q23
7q21.2
12q14.3
20q11.22
4p15.32
6q22.32
2p16.1
6p21.31
1p12
9q22.32
12q22
4q31.22
1q42.13
13q14.3
15q25.2
1p34.2
2q35
3q22.2
15q26.1
18q21.1		 ZBTB38
CDK6
HMGA2
GDF5
LCORL
LOC387103
EFEMP1
C6orf106
SPAG17
PTCH1
SOCS2
HHIP
ZNF678
DLEU7
ADAMTSL3
SCMH1
IHH
ANAPC13,CEP63
ACAN
DYM		 rs6440003-A
rs2282978-C
rs1042725-C
rs6060373-A
rs16896068-A
rs4549631-C
rs3791675-C
rs2814993-A
rs12735613-A
rs10512248-G
rs11107116-G
rs6854783-A
rs1390401-A
rs3116602-G
rs10906982-A
rs6686842-C
rs6724465-A
rs10935120-A
rs8041863-A
rs8099594-A		 0.44
0.33
0.49
0.62
0.16
0.50
0.77
0.15
0.24
0.31
0.77
0.43
0.82
0.21
0.52
0.56
0.10
0.33
0.47
0.65		 2 x 10-24
8 x 10-23
3 x 10-18
2 x 10-17
2 x 10-13
5 x 10-13
2 x 10-12
4 x 10-12
4 x 10-11
4 x 10-11
6 x 10-10
2 x 10-9
5 x 10-9
7 x 10-9
2 x 10-8
2 x 10-8
2 x 10-8
7 x 10-8
8 x 10-8
3 x 10-7 		.07 [0.04-0.09] s.d. taller - among males
.09 [0.06-0.12] s.d. taller - among males
.05 [0.03-0.08] s.d. taller - among males
.08 [0.05-0.11] s.d. shorter - among males
.07 [0.03-0.11] s.d. shorter - among males
.06 [0.03-0.08] s.d. taller - among males
.09 [0.05-0.12] s.d. taller - among males
.09 [0.05-0.13] s.d. taller - among males
.08 [0.05-0.11] s.d. shorter - among males
.05 [0.02-0.07] s.d. taller - among males
.04 [0.01-0.07] s.d. shorter - among males
.06 [0.03-0.08] s.d. taller - among males
.04 [0.01-0.08] s.d. taller - among males
.04 [0.00-0.07] s.d. shorter - among males
.05 [0.02-0.07] s.d. taller - among males
.05 [0.02-0.08] s.d. shorter - among males
.06 [0.02-0.10] s.d. shorter - among males
.06 [0.03-0.09] s.d. shorter - among males
.04 [0.01-0.06] s.d. taller - among males
.05 [0.02-0.08] s.d. taller - among males		 Affymetrix
[402,951]		 N
11/25/08 Liu
April 04, 2008
PLoS Genet
A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci. 		Psoriasis 218 cases, 519 controls 1,153 cases, 1,217 controls 6p21.33
6p21.33
13q13.3		 HLA-C
HLA-C
COG6		 rs10484554-T
rs2395029-C
rs7993214-?		 0.15
0.03
0.65		 2 x 10-39
2 x 10-26
2 x 10-6 		2.8 [2.40-3.30]
4.1 [3.10-5.30]
1.41 [1.22-1.61]		 Illumina
[305,983]		 N
11/25/08 Amos
April 03, 2008
Nat Genet
Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. 		Lung cancer 1,154 cases, 1,137 controls 2,724 cases, 3,694 controls 15q25.1
1q23.2
3q28		 CHRNA3, CHRNA5, PSMA4, LOC123688
CRP
IL1RAP		 rs8034191-G
rs2808630-G
rs7626795-G		 NR
NR
NR		 3 x 10-18
7 x 10-6
8 x 10-6 		1.3 [1.15-1.47]
1.22 [1.10-1.35]
1.16 [1.05-1.28]		 Illumina
[317,498]		 N
11/25/08 Hung
April 03, 2008
Nature
A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. 		Lung cancer 1,926 cases, 2,522 controls 2,513 cases, 4,752 controls 15q25.1 CHRNA3,CHRNA5, CHRNB4, PSMA4, LOC123688 rs8034191-C 0.34 5 x 10-20 1.3 [1.23-1.37] Illumina
[310,023]		 N
11/25/08 Thorgeirsson
April 03, 2008
Nature
A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. 		Nicotine dependence 10,995 smokers 4,848 smokers 15q25.1 CHRNA3,CHRNA5,CHRNB4 rs1051730-T 0.35 6 x 10-20 .1 [0.08-0.12] increase in cigarettes per day Illumina
[306,207]		 N
11/25/08 Tenesa
March 30, 2008
Nat Genet
Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. 		Colorectal cancer 981 cases, 1,002 controls 16,476 cases, 15,351 controls 18q21.1
8q24.21
11q23.1		 SMAD7
POU5FIP1, HsG57825, DQ515897
Intergenic		 rs4939827-T
rs7014346-A
rs3802842-C		 0.52
0.18
0.43		 8 x 10-28
9 x 10-26
6 x 10-10 		1.2 [1.16-1.24]
1.19 [1.15-1.23]
1.11 [1.08-1.15]		 Illumina
[541,628]		 N
11/25/08 Tomlinson
March 30, 2008
Nat Genet
A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. 		Colorectal cancer 922 cases, 927 controls 17,872 cases, 17,526 controls 8q23.3
10p14
8q24.21
15q13.3
18q21.1		 EIF3H
Intergenic
Intergenic
Intergenic
SMAD7		 rs16892766-A
rs10795668-A
rs6983267-?
rs4779584-?
rs4939827-?		 0.07
0.67
0.48
0.19
0.53		 3 x 10-18
3 x 10-13
7 x 10-11
5 x 10-7
2 x 10-6 		1.27 [1.20-1.34]
1.12 [1.10-1.16]
1.24 [1.17-1.33]
1.23 [1.14-1.34]
1.18 [1.10-1.25]		 Illumina
[547,647]		 N
11/25/08 Zeggini
March 30, 2008
Nat Genet
Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. 		Type 2 diabetes 4,549 cases, 5,579 controls 24,194 cases, 55,598 controls 10q25.2
7p15.1
6p22.3
10p13
12q21.1
2p21
3p14.1
1p12
10q23.33
3q27.2
12q13.2
3p25.2
9p21.3
11p15.1
6p21.1
16q12.2		 TCF7L2
JAZF1
CDKAL1
CDC123,CAMK1D
TSPAN8,LGR5
THADA
ADAMTS9
NOTCH2, ADAM30
HHEX
IGF2BP2
DCD
SYN2, PPARG
CDKN2A,CDKN2B
KCNJ11
VEGFA
FTO		 rs7903146-T
rs864745-T
rs6931514-G
rs12779790-G
rs7961581-C
rs7578597-T
rs4607103-C
rs10923931-T
rs5015480-C
rs4402960-T
rs1153188-A
rs17036101-G
rs7020996-C
rs5215-C
rs9472138-T
rs8050136-A		 NR
0.50
NR
0.18
0.27
0.90
0.76
0.11
NR
NR
0.73
0.93
NR
NR
0.28
NR		 3 x 10-23
5 x 10-14
1 x 10-11
1 x 10-10
1 x 10-9
1 x 10-9
1 x 10-8
4 x 10-8
7 x 10-8
8 x 10-8
2 x 10-7
2 x 10-7
2 x 10-7
4 x 10-7
4 x 10-6
7 x 10-6 		1.37 [1.28-1.47]
1.1 [1.07-1.13]
1.25 [1.17-1.33]
1.11 [1.07-1.14]
1.09 [1.06-1.12]
1.15 [1.10-1.20]
1.09 [1.06-1.12]
1.13 [1.08-1.17]
1.17 [1.11-1.24]
1.17 [1.10-1.25]
1.08 [1.05-1.11]
1.15 [1.10-1.21]
1.26 [1.15-1.38]
1.16 [1.09-1.23]
1.06 [1.04-1.09]
1.15 [1.09-1.22]		 Affymetrix and Illumina
[2,202,892] (imputed)		 N
11/25/08 Butcher
March 25, 2008
Behav Genet
The Nature of Nuture: A Genomewide Association Scan for Family Chaos 		Environmental confusion in the home 469 children from low chaos families,369 children from high chaos families 3,529 children NS NS NS NS NS NS Affymetrix
[117,062] (pooled)		 N
11/25/08 Capon
March 25, 2008
Hum Mol Genet
Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene. 		Psoriasis 318 cases, 288 controls 2,361 cases, 1,927 controls 6p21.33
20q13.13		 HLA-C
SPATA2		 rs3134792-?
rs495337-?		 NR
NR		 1 x 10-9
1 x 10-8 		NR
1.25 [1.12-1.39]		 Illumina
[~408,000] (pooled)		 N
11/25/08 Sullivan
March 18, 2008
Mol Psychiatry
Genomewide association for schizophrenia in the CATIE study: results of stage 1. 		Schizophrenia 738 cases, 733 controls NR 15q25.3
1q31.1
1p36.22
13q12.2
16p12.2
Xq28		 AGBL1
Intergenic
Intergenic
Intergenic
ACSM1, BUCS1
Intergenic		 rs16977195-?
rs10911902-?
rs4846033-?
rs9512730-?
rs151222-?
rs2159767-?		 0.03
0.17
0.01
0.26
0.08
0.62		 2 x 10-6
2 x 10-6
4 x 10-6
5 x 10-6
6 x 10-6
7 x 10-6 		6.01 [NR]
1.79 [NR]
2.87 [NR]
1.52 [NR]
2.1 [NR]
1.33 [NR]		 Affymetrix
[492,900]		 N
11/25/08 Gold
March 11, 2008
Proc Natl Acad Sci U S A
Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. 		Breast cancer 249 cases, 299 controls (Ashkenazi Jewish, non-BRCA1/2 carriers) 1,193 cases, 1,166 controls (Ashkenazi Jewish, non-BRCA1/2 carriers) 6q22.33 ECHDC1,RNF146 rs2180341-G 0.21 3 x 10-8 1.41 [1.25-1.59] Affymetrix
[150,080]		 N
11/25/08 Kirov
March 11, 2008
Mol Psychiatry
A genome-wide association study in 574 schizophrenia trios using DNA pooling. 		Schizophrenia 574 cases, 605 controls, 1,148 parents of cases NR 12q24.23 CCDC60 rs11064768-A 0.91 1 x 10-6 NR Illumina
[~550,000] (pooled)		 N
11/25/08 Doring
March 09, 2008
Nat Genet
SLC2A9 influences uric acid concentrations with pronounced sex-specific effects. 		Serum urate 1,644 individuals 9,947 individuals 4p16.1 SLC2A9 rs7442295-C 0.40 3 x 10-70 .35 [NR] mg/dl decrease in uric acid Affymetrix
[335,152]		 N
11/25/08 Vitart
March 09, 2008
Nat Genet
SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout. 		Serum urate 794 individuals 706 individuals 4p16.1 SLC2A9 rs737267-C 0.31 3 x 10-9 .88 [NR] uM decrease in uric acid [females only] Illumina
[308,140]		 N
11/25/08 Liu
March 05, 2008
Hum Mol Genet
Genome-wide association scans identified CTNNBL1 as a novel gene for obesity 		Obesity 1,000 individuals 896 obese individuals, 2,916 lean individuals NS NS NS NS NS NS Affymetrix
[379,319]		 N
11/25/08 Sklar
March 04, 2008
Mol Psychiatry
Whole-genome association study of bipolar disorder 		Bipolar disorder 1,461 cases, 2,008 controls 409 trios, 365 cases, 351 controls NS NS NS NS NS NS Affymetrix
[372,193]		 N
11/25/08 Hunt
March 02, 2008
Nat Genet
Newly identified genetic risk variants for celiac disease related to the immune response. 		Celiac disease 767 cases, 1,422 controls 1,643 cases, 3,406 controls 4q27
1q31.2
3q25.33
2q12.1
3q28
6q25.3
12q24.12
3p21.31		 KIAA1109, ADAD1, IL2, IL21
RGS1
IL12A, SCHIP1
IL1RL1,IL18R1,IL18RAP, SLC9A4
LPP
TAGAP
SH2B3, ATXN2
CCR1, CCR3		 rs6822844-C
rs2816316-C
rs17810546-G
rs13015714-C
rs1464510-A
rs1738074-A
rs653178-G
rs6441961-A		 0.81
NR
NR
NR
NR
NR
0.48
0.30		 3 x 10-13
3 x 10-11
1 x 10-9
4 x 10-9
5 x 10-9
7 x 10-8
8 x 10-8
3 x 10-7 		1.44 [1.30-1.58]
1.39 [1.26-1.53]
1.35 [1.23-1.49]
1.28 [1.18-1.39]
1.23 [1.15-1.32]
1.21 [1.13-1.30]
1.21 [1.13-1.30]
1.21 [1.13-1.30]		 Illumina
[310,605]		 N
11/25/08 Uhl
March 01, 2008
Arch Gen Psychiatry
Genome-wide association for methamphetamine dependence: convergent results from 2 samples 		Methamphetamine dependence 240 cases, 340 controls NR NS NS NS NS NS NS Affymetrix
[up to 466,883] (pooled)		 N
11/25/08 Blauw
February 29, 2008
Lancet Neurol
Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen 		Amyotrophic lateral sclerosis 406 cases, 404 controls NR Pending Pending Pending Pending Pending Pending Illumina
[317,503]		 Y
11/25/08 Shifman
February 15, 2008
PLoS Genet
Genome-wide association identifies a common variant in the reelin gene that increases the risk of schizophrenia only in women. 		Schizophrenia 660 cases, 2,271 controls 2,274 cases, 4,401 controls 7q22.1 RELN rs7341475-G 0.62 9 x 10-7 1.58 [1.31-1.89] Affymetrix
[510,552]		 N
11/25/08 Eeles
February 10, 2008
Nat Genet
Multiple newly identified loci associated with prostate cancer susceptibility. 		Prostate cancer 1,854 cases, 1,894 controls 3,268 cases, 3,366 controls 10q11.23
19q13.33
8q24.21
8q24.21
11q13.2
17q12
6q25.3
7q21.3
Xp11.22
3p12.1
8q24.21
17q24.3		 MSMB
KLK3
Intergenic
Intergenic
Intergenic
HNF1B
SLC22A3
LMTK2
NUDT10, NUDT11
Intergenic
Intergenic
Intergenic		 rs10993994-T
rs2735839-G
rs4242384-C
rs6983267-G
rs7931342-G
rs7501939-C
rs9364554-T
rs6465657-C
rs5945619-C
rs2660753-T
rs1016343-T
rs1859962-G		 0.40
0.85
0.09
0.49
0.51
0.57
0.29
0.46
0.36
0.11
0.18
0.46		 9 x 10-29
2 x 10-18
3 x 10-16
9 x 10-13
2 x 10-12
9 x 10-12
6 x 10-10
1 x 10-9
2 x 10-9
3 x 10-8
1 x 10-7
1 x 10-6 		1.25 [1.17-1.34]
1.2 [1.10-1.33]
1.88 [NR]
1.42 [NR]
1.19 [1.11-1.27]
1.41 [NR]
1.17 [1.08-1.26]
1.12 [1.05-1.20]
1.19 [1.07-1.31]
1.18 [1.06-1.31]
1.37 [NR]
1.26 [NR]		 Illumina
[541,129]		 N
11/25/08 Gudmundsson
February 10, 2008
Nat Genet
Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. 		Prostate cancer 1,854 cases, 21,372 controls 8,239 cases, 7,590 controls Xp11.22
2p15		 NUDT10, NUDT11, LOC340602, GSPT2, MAGED1
EHBP1		 rs5945572-A
rs721048-A		 0.35
0.19		 4 x 10-13
8 x 10-9 		1.23 [1.16-1.30]
1.15 [1.10-1.21]		 Illumina
[310,520]		 N
11/25/08 Thomas
February 10, 2008
Nat Genet
Multiple loci identified in a genome-wide association study of prostate cancer. 		Prostate cancer 1,172 cases, 1,157 controls 3,941 cases, 3,964 controls 8q24.21
10q11.23
8q24.21
17q12
11q13.2
10q26.13
7p15.2		 Intergenic
MSMB
Intergenic
HNF1B
Intergenic
CTBP2
JAZF1		 rs4242382-A
rs10993994-T
rs6983267-G
rs4430796-A
rs10896449-G
rs4962416-C
rs10486567-G		 0.12
0.40
0.53
0.54
0.52
0.27
0.77		 3 x 10-19
7 x 10-13
7 x 10-12
1 x 10-9
2 x 10-9
2 x 10-7
2 x 10-6 		1.66 [1.47-1.87]
1.16 [1.04-1.29]
1.28 [1.15-1.45]
1.18 [1.04-1.32]
1.1 [0.98-1.23]
1.17 [1.05-1.30]
1.12 [1.02-1.25]		 Illumina
[527,869]		 N
11/25/08 Sandhu
February 09, 2008
Lancet
LDL-cholesterol concentrations: a genome-wide association study. 		LDL cholesterol 11,685 individuals 5,036 individuals 1p13.3
19q13.32
2p24.1		 CELSR2,PSRC1
APOC1
APOB		 rs599839-G
rs4420638-G
rs562338-T		 0.19
0.18
0.20		 1 x 10-33
1 x 10-20
1 x 10-9 		.16 [0.14-0.18] mmol/L decrease
.06 [0.04-0.08] mmol/L increase
.04 [0.02-0.06] mmol/L decrease		 Affymetrix and Illumina
[up to 461,986]		 N
11/25/08 Uda
February 05, 2008
Proc Natl Acad Sci U S A
Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia. 		Fetal hemoglobin levels 4,305 individuals 521 individuals 2p15
11p15.4		 BCL11A
HBB		 rs11886868-T
rs4910742-A		 0.80
0.93		 7 x 10-35
1 x 10-21 		.48 [NR] s.d. decrease in HbF
.58 [NR] s.d. decrease in HbF		 Affymetrix
[362,129]		 N
11/25/08 Kong
February 02, 2008
Science
Sequence variants in the RNF212 gene associate with genome-wide recombination rate. 		Recombination rate (females) 1,702 women 1,663 women 4p16.3 RNF212,SPON2 rs1670533-C 0.23 (men and women combined) 2 x 10-12 88.2 [63.7-112.7] cM increase Illumina
[309,241]		 N
11/25/08 " Recombination rate (males) 1,887 men 1,248 men 4p16.3 RNF212,SPON2 rs3796619-T 0.33 (men and women combined) 3 x 10-24 70.7 [57.1-84.3] cM decrease Illumina
[309,241]		 N
12/11/08 Berrettini
January 29, 2008
Mol Psychiatry
Alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking 		Nicotine dependence 7,481 individuals ~2000 individuals NS NS NS NS NS NS Affymetrix
[460,959]		 N
11/25/08 Kayser
January 24, 2008
Am J Hum Genet
Three genome-wide association studies and a linkage analysis identify HERC2 as a human iris color gene. 		Iris color 1,406 individuals 8,273 individuals 15q13.1 HERC2 rs916977-? NR 1 x 10-43 NR Affymetrix and Illumina
[up to ~500,000] (pooled)		 N
11/25/08 Butcher
January 22, 2008
Genes Brain Behav
Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays 		General cognitive ability 458 low g, 402 high g twin children (unrelated) 3,195 twin children (unrelated) NS NS NS NS NS NS Affymetrix
[449,127] (pooled)		 N
11/25/08 Harley
January 20, 2008
Nat Genet
Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. 		Systemic lupus erythematosus 720 female cases, 2,337 female controls 1,846 female cases, 1,825 female controls 6p21.33
16p11.2
7q32.1
11p15.5
3p14.3
1q25.1		 HLA region
ITGAM
IRF5, TNPO3
KIAA1542
PXK
Intergenic		 rs3131379-A
rs9888739-T
rs12537284-A
rs4963128-?
rs6445975-C
rs10798269-?		 0.1
0.13
0.13
0.34
0.28
0.64		 2 x 10-52
2 x 10-23
4 x 10-19
3 x 10-10
7 x 10-9
1 x 10-7 		2.36 [2.11-2.64]
1.62 [1.47-1.78]
1.54 [1.40-1.70]
1.28 [1.18-1.37]
1.25 [1.16-1.35]
1.22 [1.14-1.32]		 Illumina
[317,501]		 N
11/25/08 Hom
January 20, 2008
N Engl J Med
Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. 		Systemic lupus erythematosus 1,311 cases, 3,340 controls 793 cases, 857 controls 6p21.32
2q32.3
7q32.1
16p11.2
8p23.1
9q34.13
5p12
18q22.3
1p31.1		 HLA-DQA1
STAT4
IRF5, TNPO3
ITGAM, ITGAX
C8orf13, BLK
NTNG2
GHR
SOCS6
NEGR1		 rs2187668-A
rs7574865-T
rs10488631-C
rs11574637-C
rs13277113-A
rs11243676-A
rs979233-T
rs17083844-A
rs12141391-A		 0.11
0.23
0.12
0.19
0.23
0.07
0.46
0.03
0.02		 3 x 10-21
9 x 10-14
2 x 10-11
3 x 10-11
1 x 10-10
3 x 10-6
4 x 10-6
6 x 10-6
7 x 10-6 		NR
NR
NR
1.33 [1.22-1.46]
1.39 [1.28-1.51]
NR
NR
NR
NR		 Illumina
[502,033]		 N
11/25/08 Kozyrev
January 20, 2008
Nat Genet
Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus. 		Systemic lupus erythematosus 279 cases, 515 controls 1,757 cases, 1,540 controls 4q24 BANK1 rs10516487-G 0.77 4 x 10-10 1.38 [1.25-1.53] Affymetrix
[85,042]		 N
11/25/08 Hakonarson
January 15, 2008
Diabetes
A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study. 		Type 1 diabetes 467 trios, 561 cases, 1,143 controls 549 families, 364 trios 12q13.2 RAB5B, SUOX, IKZF4, ERBB3, CDK2 rs1701704-C 0.35 9 x 10-10 1.25 [1.12-1.40] Illumina
[543,071]		 N
11/25/08 Byun
January 14, 2008
Arch Neurol
Genome-Wide Pharmacogenomic Analysis of the Response to Interferon Beta Therapy in Multiple Sclerosis 		Response to interferon beta therapy 206 multiple sclerosis cases NR NS NS NS NS NS NS Affymetrix
[~100,000] (pooled)		 N
11/25/08 Kathiresan
January 13, 2008
Nat Genet
Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. 		HDL cholesterol 2,758 individuals 18,544 individuals 16q13
15q22.1
8p21.3
1q42.13
9q31.1
18q21.1		 CETP
LIPC
LPL
GALNT2
ABCA1
LIPG, ACAA2		 rs1800775-C
rs1800588-T
rs328-G
rs4846914-G
rs3890182-A
rs2156552-A		 0.51
0.21
0.09
0.40
0.13
0.18		 1 x 10-73
2 x 10-32
9 x 10-23
2 x 10-13
3 x 10-10
2 x 10-7 		.18 [0.16-0.20]% SD lower
.14 [0.12-0.16]% SD higher
.17 [0.13-0.21]% SD higher
.07 [0.05-0.09] % SD lower
.1 [0.06-0.14]% SD lower
.07 [0.05-0.09]% SD lower		 Affymetrix
[389,878]		 N
11/25/08 " LDL cholesterol 2,758 individuals 18,544 individuals 19q13.32
19p13.2
1p32.3
1p13.3
2p24.1
5q13.3
19p13.11		 APOE, APOC1, APOC4, APOC2
LDLR
PCSK9
CELSR2,PSRC1,SORT1
APOB
HMGCR
CILP2, PBX4		 rs4420638-G
rs6511720-T
rs11591147-T
rs646776-C
rs693-A
rs12654264-T
rs16996148-T		 0.20
0.10
0.01
0.24
0.48
0.39
0.10		 1 x 10-60
2 x 10-51
2 x 10-44
3 x 10-29
1 x 10-21
1 x 10-20
3 x 10-8 		.19 [0.15-0.23] % SD higher
.26 [0.22-0.30] % SD lower
.47 [0.41-0.53] % SD lower
.16 [0.14-0.18] % SD lower
.12 [0.10-0.14] % SD higher
.1 [0.08-0.12] % SD higher
.1 [0.06-0.14] % SD lower		 Affymetrix
[389,878]		 N
11/25/08 " Triglycerides 2,758 individuals 18,544 individuals 8p21.3
7q11.23
11q23.3
8q24.13
1q42.13
2p23.3
19p13.11
1p31.3
2p24.1		 LPL
BCL7B, TBL2, MLXIPL
APOA1, APOC3, APOA4, APOA5, ZNF259, BUD13
TRIB1
GALNT2
GCKR
CILP2, PBX4
ANGPTL3, DOCK7, ATG4C
APOB		 rs328-G
rs17145738-T
rs28927680-G
rs17321515-G
rs4846914-G
rs780094-T
rs16996148-T
rs12130333-T
rs693-A		 0.09
0.13
0.07
0.49
0.40
0.34
0.10
0.22
0.48		 2 x 10-28
7 x 10-22
2 x 10-17
4 x 10-17
7 x 10-15
3 x 10-14
4 x 10-9
2 x 10-8
2 x 10-7 		.19 [0.15-0.23]% SD lower
.14 [0.25-0.53] % SD lower
.26 [0.20-0.32]% SD higher
.08 [0.06-0.10] % SD lower
.08 [0.06-0.10] % SD higher
.13 [0.09-0.17]% SD higher
.1 [0.06-0.14] % SD lower
.11 [0.07-0.15] % SD lower
.08 [0.04-0.12]% SD higher		 Affymetrix
[389,878]		 N
11/25/08 Kooner
January 13, 2008
Nat Genet
Genome-wide scan identifies variation in MLXIPL associated with plasma triglycerides. 		Triglycerides 2,011 individuals 10,536 individuals 11q23.3
8p21.3
7q11.23
11q23.3		 LOC440069, MGC13125
LPL, C8orf35, SLC18A1
MLXIPL
APOA1,KIAA0999,LOC645044		 rs1558861-C
rs326-A
rs3812316-C
rs2075292-G		 0.18
0.78
0.95
0.24		 2 x 10-26
5 x 10-12
1 x 10-10
5 x 10-8 		17 [13.28-20.72] % higher
6.6 [3.66-9.54] % higher
10.5 [5.3-17.7]% higher
8.7 [5.76-11.64] % higher		 Perlegen
[up to 216,774]		 N
11/25/08 Sanna
January 13, 2008
Nat Genet
Common variants in the GDF5-UQCC region are associated with variation in human height. 		Height 6,669 individuals 28,801 individuals 20q11.22
4q12
15q26.1
3q23
5q14.1		 BFZB
PDGFRA
POLG
ZBTB38
HOMER1		 rs6060369-C
rs17690232-C
rs4932217-A
rs724016-G
rs10078095-C		 0.44
0.80
0.58
0.36
0.22		 2 x 10-16
4 x 10-7
8 x 10-7
1 x 10-6
3 x 10-6 		.44 [NR] cm taller
.86 [NR] cm taller
.66 [NR] cm taller
.61 [NR] cm taller
.9 [NR] cm taller		 Illumina and Affymetrix
[~2,261,000] (imputed)		 N
11/25/08 Willer
January 13, 2008
Nat Genet
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. 		HDL cholesterol 8,656 individuals 11,399 individuals 16q13
16q13
16q13
15q22.1
8p21.3
1q42.13
18q21.1
9q31.1
12q24.11
16q22.1		 CETP
CETP
CETP
LIPC
LPL
GALNT2
LIPG
ABCA1
MVK,MMAB
LCAT		 rs3764261-A
rs1864163-G
rs9989419-G
rs4775041-C
rs10503669-A
rs2144300-T
rs2156552-T
rs4149268-C
rs2338104-G
rs255052-A		 0.31
0.80
0.65
0.33
0.10
0.60
0.84
0.64
0.45
0.17		 2 x 10-57
7 x 10-39
3 x 10-31
3 x 10-20
4 x 10-19
3 x 10-14
6 x 10-12
1 x 10-10
3 x 10-8
1 x 10-7 		3.47 [NR] mg/dl higher
4.12 [NR] mg/dl higher
1.72 [NR] mg/dl higher
1.38 [NR] mg/dl higher
2.09 [NR] mg/dl higher
1.11 [NR] mg/dl higher
1.2 [NR] mg/dl higher
.82 [NR] mg/dl higher
.48 [NR] mg/dl higher
.74 [NR] mg/dl higher		 Illumina and Affymetrix
[~2,261,000] (imputed)		 N
11/25/08 " LDL cholesterol 8,589 individuals 7,440-10,783 individuals 19q13.32
1p13.3
19p13.2
2p24.1
1p32.3
19p13.11
6p21.32		 APOE,APOC1,APOC4
CELSR2,PSRC1,SORT1
LDLR
APOB
PCSK9
NCAN,CILP2
B3GALT4		 rs4420638-G
rs599839-A
rs6511720-G
rs562338-G
rs11206510-T
rs16996148-G
rs2254287-G		 0.18
0.77
0.90
0.82
0.81
0.89
0.38		 3 x 10-43
6 x 10-33
4 x 10-26
6 x 10-22
4 x 10-11
3 x 10-9
5 x 10-8 		6.61 [NR] mg/dl higher
5.48 [NR] mg/dl higher
9.17 [NR] mg/dl higher
4.89 [NR] mg/dl higher
3.04 [NR] mg/dl higher
3.32 [NR] mg/dl higher
1.91 [NR] mg/dl higher		 Illumina and Affymetrix
[~2,261,000] (imputed)		 N
11/25/08 " Triglycerides 8,684 individuals 5,312-9,707 individuals 2p23.3
11q23.3
8p21.3
8q24.13
7q11.23
1p31.3
19p13.11
15q22.1
1q42.13		 GCKR
APOA5, APOA4, APOC3, APOA1
LPL
TRIB1
MLXIPL
ANGPTL3
NCAN,CILP2
LIPC
GALNT2		 rs780094-T
rs12286037-T
rs10503669-C
rs17321515-A
rs17145738-C
rs1748195-C
rs16996148-G
rs4775041-C
rs2144300-C		 0.39
0.06
0.90
0.56
0.84
0.70
0.92
0.33
0.40		 6 x 10-32
1 x 10-26
4 x 10-22
7 x 10-13
2 x 10-12
2 x 10-10
3 x 10-9
2 x 10-8
8 x 10-7 		8.59 [NR] mg/dl higher
25.82 [NR] mg/dl higher
11.57 [NR] mg/dl higher
6.42 [NR] mg/dl higher
8.21 [NR] mg/dl higher
7.12 [NR] mg/dl higher
6.1 [NR] mg/dl higher
3.62 [NR] mg/dl higher
4.25 [NR] mg/dl higher		 Illumina and Affymetrix
[~2,261,000]] (imputed)		 N
11/25/08 Wallace
January 10, 2008
Am J Hum Genet
Genome-wide association study identifies genes for biomarkers of cardiovascular disease: serum urate and dyslipidemia. 		LDL cholesterol 1,955 hypertensive individuals 2,033 individuals in 519 families; 1,461 twins (1/pair selected randomly) 11q23.3
1p13.3
2p23.3		 APOA1,APOC3,APOA5
CELSR2,PSRC1
GCKR		 rs6589566-G
rs599839-G
rs780094-T		 0.06
0.24
0.39		 3 x 10-11
1 x 10-7
5 x 10-7 		NR
.95 [0.93-0.97]
NR		 Affymetrix
[400,496]		 N
11/25/08 " Serum urate 1,955 hypertensive individuals 2,033 individuals in 519 families; 1,461 twins (1/pair selected randomly) 4p16.1 SLC2A9,WDR1 rs7442295-A 0.79 2 x 10-15 .02 [0.02-0.03] mMol/L higher Affymetrix
[400,496]		 N
11/25/08 Hinney
December 26, 2007
PLoS One
Genome wide association (GWA) study for early onset extreme obesity supports the role of fat mass and obesity associated gene (FTO) variants. 		Obesity (early onset extreme) 487 young cases, 442 controls 2,269 individuals in 644 families 16q12.2 FTO rs1121980-T 0.41 1 x 10-7 1.66 [1.37-2.01] Affymetrix
[440,794]		 N
11/25/08 Duggan
December 19, 2007
J Natl Cancer Inst
Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP 		Prostate cancer 1,235 cases, 1,599 controls 1,242 cases, 917 controls NS NS NS NS NS NS Illumina & Affymetrix
[60,275]		 N
11/25/08 van Es
December 16, 2007
Nat Genet
Genetic variation in DPP6 is associated with susceptibility to amyotrophic lateral sclerosis. 		Amyotrophic lateral sclerosis 737 cases, 721 controls 1,030 cases, 1,195 controls 7q36.2
15q22.1
2p24.2		 DPP6
LIPC
Intergenic		 rs10260404-C
rs3825776-?
rs7580332-?		 0.35
0.29
0.45		 5 x 10-8
9 x 10-6
9 x 10-6 		1.3 [1.18-1.43]
1.34 [1.20-1.46]
1.22 [1.09-1.35]		 Illumina
[311,946]		 N
11/25/08 Cronin
December 07, 2007
Hum Mol Genet
A genome-wide association study of sporadic ALS in a homogenous Irish population. 		Amyotrophic lateral sclerosis 221 cases, 211 controls 737 cases, 721 controls 7q36.2 DPP6 rs10260404-? 0.37 3 x 10-6 1.37 [1.20-1.56] Illumina
[497,917]		 N
11/25/08 Suzuki
November 17, 2007
Pharmacogenet Genomics
A novel genetic marker for coronary spasm in women from a genome-wide single nucleotide polymorphism analysis. 		Coronary spasm 50 Japanese female cases, 50 Japanese female controls 151 Japanese female cases, 160 Japanese female controls 14q21.1 Intergenic rs10498345-T 0.30 9 x 10-7 2.33 [1.64-3.23] Affymetrix
[97,552]		 N
11/25/08 Li
November 12, 2007
Arch Neurol
Candidate single-nucleotide polymorphisms from a genomewide association study of Alzheimer disease. 		Alzheimer's disease 753 cases, 736 controls 418 cases, 249 controls 19q13.32 APOE, APOC1 rs4420638-? NR 2 x 10-44 NR Affymetrix
[469,438]		 N
11/25/08 Li
November 09, 2007
PLoS Genet
The GLUT9 gene is associated with serum uric acid levels in Sardinia and Chianti cohorts. 		Serum urate 4,305 Sardinian individuals 1,301 Tuscan individuals 4p16.1 GLUT9 rs6855911-A 0.74 2 x 10-16 .32 [NR] mg/dl higher Affymetrix
[362,129]		 N
11/25/08 Plenge
November 04, 2007
Nat Genet
Two independent alleles at 6q23 associated with risk of rheumatoid arthritis 		Rheumatoid arthritis 397 cases, 1,211 Framingham individuals 2,283 cases, 3,258 controls 6q23.3
6q23.3		 TNFAIP3, OLIG3
TNFAIP3, OLIG3		 rs10499194-C
rs6920220-?		 0.71
0.20		 1 x 10-9
1 x 10-7 		1.33 [1.15-1.52]
1.22 [NR]		 Affymetrix
[79,853]		 N
11/25/08 Webster
November 01, 2007
Neurodegener Dis
Sorl1 as an Alzheimer's disease predisposition gene? 		Alzheimer's disease 664 cases, 422 controls NR 19q13.32 APOE rs4420638-? NR 1 x 10-39 NR Affymetrix
[~502,627]		 N
11/25/08 Sulem
October 21, 2007
Nat Genet
Genetic determinants of hair, eye and skin pigmentation in Europeans. 		Blond vs. brown hair color 2,986 individuals 3,932 individuals 14q32.12
15q13.1
12q21.33
16q24.3		 SLC24A4
OCA2
KITLG
MC1R		 rs12896399-T
rs1667394-A
rs12821256-C
rs1805007-T		 0.44
0.88
0.14
0.08		 1 x 10-48
6 x 10-35
4 x 10-30
2 x 10-13 		2.56 [2.12-3.09]
4.94 [3.16-7.71]
2.32 [1.86-2.92]
2.34 [1.69-3.24]		 Illumina
[317,511]		 N
02/16/09 " Blue vs. brown eyes 2,986 individuals 3,932 individuals 15q13.1 OCA2 rs1667394-A 0.88 1 x 10-241 29.43 [21.47-40.35] Illumina
[317,511]		 N
11/25/08 " Blue vs. green eyes 2,986 individuals 3,932 individuals 15q13.1
14q32.12
11q14.3		 OCA2
SLC24A4
TYR		 rs1667394-A
rs12896399-T
rs1393350-A		 0.98
0.40
0.23		 2 x 10-53
4 x 10-38
3 x 10-12 		6.74 [4.61-9.83]
2.06 [1.76-2.42]
1.52 [1.28-1.81]		 Illumina
[317,511]		 N
11/25/08 " Freckles 2,986 individuals 3,932 individuals 16q24.3
6p25.3
11q14.3		 MC1R
SEC5L1,IRF4
TYR		 rs1805007-T
rs1540771-A
rs1042602-C		 0.05
0.42
0.67		 1 x 10-96
4 x 10-18
2 x 10-11 		4.37 [3.56-5.37]
1.4 [1.26-1.57]
1.32 [1.17-1.49]		 Illumina
[317,511]		 N
02/16/09 " Red vs non-red hair color 2,986 individuals 3,932 individuals 16q24.3 MC1R rs1805007-T NR 2 x 10-142 12.47 [9.37-16.60] Illumina
[317,511]		 N
02/16/09 " Skin sensitivity to sun 2,986 individuals 3,932 individuals 16q24.3
11q14.3		 MC1R
TYR		 rs1805007-T
rs1393350-A		 0.06
0.27		 2 x 10-55
2 x 10-6 		2.94 [2.42-3.58]
1.26 [1.11-1.43]		 Illumina
[317,511]		 N
11/25/08 Stokowski
October 15, 2007
Am J Hum Genet
A genomewide association study of skin pigmentation in a South Asian population. 		Skin pigmentation 363 with maxL* < 56 and 374 with maxL* > 63; 20% tails of distribution 116 low maxL*, 115 high maxL* individuals 15q21.1
5p13.3
11q14.3		 SLC24A5
SLC45A2
TYR		 rs1834640-G
rs16891982-C
rs1042602-C		 0.08
0.83
0.84		 1 x 10-50
3 x 10-11
4 x 10-10 		12.5 [8.33-20.0]
4.86 [2.88-8.21]
4.36 [2.64-7.20]		 Perlegen
[1,502,205] (pooled)		 N
11/25/08 Broderick
October 14, 2007
Nat Genet
A genome-wide association study shows that common alleles of SMAD7 influence colorectal cancer risk. 		Colorectal cancer 940 cases, 965 controls 7,473 cases, 5,984 controls 18q21.1 SMAD7 rs4939827-T 0.52 1 x 10-12 1.16 [1.09-1.27] Illumina
[547,647]		 N
11/25/08 Cervino
October 08, 2007
Ann N Y Acad Sci
A genome-wide study of lupus: preliminary analysis and data release 		Lupus 51 cases, 114 controls NR NS NS NS NS NS NS Affymetrix
[241,701]		 N
11/25/08 Benjamin
September 19, 2007
BMC Med Genet
Genome-wide association with select biomarker traits in the Framingham Heart Study. 		Select biomarker traits 1,012 individuals (Framingham) NR 1q23.2
1q23.2
1q23.2
1p31.1
19q12
10q26.2
15q21.3
4q31.1
5q23.2
6q15
1q23.2
9q21.32
10q21.1
13q14.11
6q21
7p13
1q23.2
11q23.2
13q21.1
7p21.3
14q23.2		 FCER1A,OR10J3
OR10J1
CRP
Intergenic
ZNF536
PTPRE, MKI67
Intergenic
CLGN, ELMOD2
Intergenic
Intergenic
IGSF4B
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
IGSF4B
DRD2
Intergenic
Intergenic
Intergenic		 rs2494250-?
rs4128725-?
rs2794520-?
rs7552393-?
rs746961-?
rs2387326-?
rs10518765-?
rs17532515-?
rs1119582-?
rs10485165-?
rs10489849-?
rs1998303-?
rs583012-?
rs10492681-?
rs1417352-?
rs1486139-?
rs1474747-?
rs1079596-?
rs10507577-?
rs7778619-?
rs8005745-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-14 (MCP1)
4 x 10-12 (MCP1)
3 x 10-8 (CRP average 2,6,7)
5 x 10-7 (TNFA)
8 x 10-7 (CRP6)
1 x 10-6 (VitKPhylloq)
1 x 10-6 (AlkPhos)
1 x 10-6 (Bilirubin)
1 x 10-6 (CRP average 2,6,7)
1 x 10-6 (VitD25OH)
1 x 10-6 (MCP1)
1 x 10-6 (AAT)
2 x 10-6 (CRP2)
2 x 10-6 (ALT2)
2 x 10-6 (ANP6)
2 x 10-6 (ANP6)
3 x 10-6 (MCP1)
3 x 10-6 (ANP6)
3 x 10-6 (VitD25OH)
3 x 10-6 (CD40L)
4 x 10-6 (CD40L)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Fox
September 19, 2007
BMC Med Genet
Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. 		Body mass index 1,341 individuals (Framingham) NR 7q32.3
7q23.3
13q21.32		 Intergenic
Intergenic
Intergenic		 rs1106683-?
rs1106684-?
rs1333026-?		 NR
NR
NR		 1 x 10-7
2 x 10-6
8 x 10-6 		NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Waist circumference 1,341 individuals (Framingham) NR 8q21.1
3q13.31		 GDAP1
Intergenic		 rs4471028-?
rs1875517-?		 NR
NR		 2 x 10-7
2 x 10-6 		NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Gottlieb
September 19, 2007
BMC Med Genet
Genome-wide association of sleep and circadian phenotypes. 		Sleep duration 738 individuals (Framingham) NR 3p22.1
13q21.2		 MYRIP
Intergenic		 rs6599077-?
rs10492604-?		 NR
NR		 1 x 10-7
4 x 10-6 		NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Sleepiness 738 individuals (Framingham) NR 5q11.2
8q13.3		 PDE4D
EYA1		 rs1823068-?
rs2218488-?		 NR
NR		 3 x 10-8 (sleepiness)
3 x 10-6 (sleepiness)		 NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Hwang
September 19, 2007
BMC Med Genet
A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study. 		Cystatin C 810-1,010 individuals depending on measure (Framingham) NR 20p11.21 CST9L, CST9, CST3 rs1158167-? NR 9 x 10-9 NR Affymetrix
[70,897]		 N
11/25/08 " Thyroid stimulating hormone 810-1,010 individuals depending on measure (Framingham) NR 7p15.3
6q21
7p15.3		 Intergenic
HACE1
RAPGEF5		 rs6977660-?
rs9322817-?
rs10499559-?		 NR
NR
NR		 4 x 10-6
7 x 10-6
8 x 10-6 		NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Urinary albumin excretion 810-1,010 individuals depending on measure (Framingham NR 11q23.2
21q21.3		 FAM55B
Intergenic		 rs1712790-?
rs9305354-?		 NR
NR		 2 x 10-6
8 x 10-6 		NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Kathiresan
September 19, 2007
BMC Med Genet
A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study 		Blood lipid traits 1,087 individuals (Framingham) ~8,100 individuals NS NS NS NS NS NS Affymetrix
[70,897]		 N
11/25/08 Kiel
September 19, 2007
BMC Med Genet
Genome-wide association with bone mass and geometry in the Framingham Heart Study. 		Bone mineral density 1,141 individuals (Framingham) NR 13q21.31
16q23.3
10p15.2
12q21.1
20q11.23
4p16.1
3p24.1
7q35		 Intergenic
Intergenic
Intergenic
Intergenic
CTNNBL1
Intergenic
RBMS3
CNTNAP2		 rs9317284-?
rs4087296-?
rs2165468-?
rs10506701-?
rs4811196-?
rs9291683-?
rs10510628-?
rs2214681-?		 NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7 (FNBMDm)
3 x 10-7 (TRBMDf)
1 x 10-6 (FNBMDm)
1 x 10-6 (TRBMD)
1 x 10-6 (TRBMDf)
2 x 10-6 (BUA)
3 x 10-6 (TRBMDm)
3 x 10-6 (BUA)		 NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Hip geometry 1,141 individuals (Framingham) NR 12q21.31
5p14.1
8p12
5q14.3
3q12.3
1p11.2
3p14.3
5q13.2
11q14.1
18q12.1
3p14.1
12p13.31
13q13.3
6p24.1
11q23.2
3p24.3		 Intergenic
Intergenic
NRG1
GPR98
Intergenic
Intergenic
ERC2
ZNF366
Intergenic
Intergenic
Intergenic
VAMP1
Intergenic
PHACTR1
Intergenic
KCNH8		 rs10506821-?
rs2548003-?
rs10503887-?
rs10514345-?
rs991258-?
rs6600671-?
rs2054989-?
rs10515148-?
rs1452928-?
rs4131805-?
rs922948-?
rs10492096-?
rs1590305-?
rs4715166-?
rs638882-?
rs2053506-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7 (ShaftW1f)
2 x 10-7 (NeckZ1rf)
2 x 10-7 (ShaftZ1R)
2 x 10-7 (NeckZ1)
5 x 10-7 (ShaftW1)
6 x 10-7 (NeckZ1rf)
6 x 10-7 (NeckW1rf)
6 x 10-7 (NeckZ1rf)
7 x 10-7 (ShaftW1f)
2 x 10-6 (NSAm)
2 x 10-6 (ShaftW1f)
3 x 10-6 (ShaftZ1rf)
3 x 10-6 (NeckZ1rm)
3 x 10-6 (NeckW1rf)
4 x 10-6 (NeckZ1rf)
4 x 10-6 (NeckZ1)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Larson
September 19, 2007
BMC Med Genet
Framingham Heart Study 100K project: genome-wide associations for cardiovascular disease outcomes. 		Atrial fibrillation 1,341-1,345 individuals, depending on measure (Framingham) NR 13q14.12
15q23
11q22.1		 Intergenic
Intergenic
CNTN5		 rs958546-?
rs4776472-?
rs10501920-?		 NR
NR
NR		 5 x 10-6
8 x 10-6
9 x 10-6 		NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Heart failure 1,341-1,345 individuals, depending on measure (Framingham NR 10q25.3 KIAA1598 rs740363-? NR 9 x 10-6 NR Affymetrix
[70,897]		 N
11/25/08 " Major CVD 1,341-1,345 individuals, depending on measure (Framingham) NR 6p24.1 Intergenic rs499818-? NR 7 x 10-6 (major CVD) NR Affymetrix
[70,897]		 N
11/25/08 Levy
September 19, 2007
BMC Med Genet
Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness 		Blood pressure 644-1,327 individuals, depending on measure (Framingham) NR 16q23.3
2q36.3
1p31.3
14q24.3
8q13.3
3p26.3
5q22.1
14q24.3
6q15		 CDH13
CCL20, WDR69
Intergenic
Intergenic
Intergenic
CNTN4
CAMK4
C14orf118
Intergenic		 rs3096277-?
rs7591163-?
rs10493340-?
rs935334-?
rs1963982-?
rs4370013-?
rs10491334-?
rs2121070-?
rs2509458-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-9 (SBPLTA)
3 x 10-7 (DBPLTA)
2 x 10-6 (SBP)
3 x 10-6 (DBP)
3 x 10-6 (DBP)
4 x 10-6 (DBP)
4 x 10-6 (DBP)
5 x 10-6 (DBP)
7 x 10-6 (DBP)		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Tonometry 644-1,327 individuals, depending on measure (Framingham NR 3p24.1
20q13.13
8p22
13q31.3
2q14.3
5q14.3
17p12
1q25.1
3q24
3p22.3
9q31.2
6q25.2
7q33		 TGFBR2
PREX1
VPS37A
GPC6
CNTNAP5
MEF2C
HS3ST3A1
TNR
SLC9A9
Intergenic
Intergenic
SYNE1
EXOC4		 rs3773643-?
rs6063312-?
rs3793427-?
rs6492654-?
rs1367248-?
rs770189-?
rs10521232-?
rs3766680-?
rs1371924-?
rs10514688-?
rs7042864-?
rs1322512-?
rs10488172-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 2 x 10-7 (MAPLTA)
2 x 10-6 (RW)
2 x 10-6 (FWLTA)
2 x 10-6 (RWLTA)
3 x 10-6 (CF-PWVLTA)
3 x 10-6 (CB-PWV)
4 x 10-6 (CF-PWVLTA)
4 x 10-6 (FWLTA)
4 x 10-6 (RWLTA)
6 x 10-6 (CB-PWV)
6 x 10-6 (CB-PWV)
8 x 10-6 (MAP)
8 x 10-6 (RWLTA)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Lunetta
September 19, 2007
BMC Med Genet
Genetic correlates of longevity and selected age-related phenotypes: a genome-wide association study in the Framingham Study. 		Aging traits 1,345 individuals (Framingham) NR 2p12
12p11.22
11q14.3
2p12
12q24.23
2q24.1
7q21.11
1q42.3
15q25.3
3q25.31		 Intergenic
Intergenic
Intergenic
Intergenic
CCDC60
GALNT13
Intergenic
GNG4
KLHL25
KCNAB1		 rs10496265-?
rs1463605-?
rs1528753-?
rs10496262-?
rs7137869-?
rs958672-?
rs2371208-?
rs291353-?
rs7176093-?
rs3772255-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-8 (age at natural menopause)
7 x 10-8 (biologic age)
8 x 10-8 (age at death)
3 x 10-7 (age at natural menopause)
6 x 10-7 (walking speed exam 7)
2 x 10-6 (age at natural menopause)
3 x 10-6 (age at death)
6 x 10-6 (age at natural menopause)
7 x 10-6 (biologic age)
8 x 10-6 (biologic age)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Morbidity-free survival 1,345 individuals (Framingham) NR 1q24.2
5p15.32
6p24.3
8p22
16q21		 DPT
Intergenic
Intergenic
Intergenic
Intergenic		 rs1412337-?
rs32566-?
rs10484246-?
rs4831837-?
rs2639889-?		 NR
NR
NR
NR
NR		 2 x 10-9
2 x 10-9
8 x 10-8
5 x 10-7
9 x 10-7 		NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Meigs
September 19, 2007
BMC Med Genet
Genome-wide association with diabetes-related traits in the Framingham Heart Study. 		Diabetes (incident) 1,087 individuals (Framingham) NR 2q32.3 TMEFF2 rs10497721-? NR 7 x 10-7 NR Affymetrix
[70,897]		 N
11/25/08 " Diabetes related insulin traits 1,087 individuals (Framingham) NR 14q12
14q12
7p15.1
13q21.33		 Intergenic
Intergenic
CPVL
Intergenic		 rs2877832-?
rs2877832-?
rs10486607-?
rs2066219-?		 NR
NR
NR
NR		 2 x 10-6 (FI)
3 x 10-6 (HOMA-IR)
8 x 10-6 (HbA1C)
9 x 10-6 (ISI_0-120)		 NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Fasting plasma glucose 1,087 individuals (Framingham) NR 8p11.21
3p24.1
4q27
4q27
5q23.3
8p11.21		 ZMAT4
Intergenic
PRDM5
PRDM5
Intergenic
ZMAT4		 rs2722425-?
rs10510634-?
rs180730-?
rs180730-?
rs7731657-?
rs2722425-?		 NR
NR
NR
NR
NR
NR		 2 x 10-8 (tFPG)
5 x 10-6 (tFPG)
5 x 10-6 (FPG)
6 x 10-6 (tFPG)
7 x 10-6 (tFPG)
9 x 10-6 (FPG)		 NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Murabito
September 19, 2007
BMC Med Genet
A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study. 		Breast cancer 1,345 individuals (Framingham) NR 17q21.33
5q34
12q21.1
18q21.2
13q32.1
7q11.22
2p16.1
15q21.1
21q21.3		 COL1A1
Intergenic
Intergenic
Intergenic
ABCC4
Intergenic
Intergenic
FBN1
GRIK1		 rs2075555-?
rs6556756-?
rs1154865-?
rs1978503-?
rs1926657-?
rs10263639-?
rs10490113-?
rs1876206-?
rs458685-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR		 8 x 10-8
5 x 10-7
7 x 10-7
1 x 10-6
2 x 10-6
3 x 10-6
5 x 10-6
6 x 10-6
6 x 10-6 		NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Prostate cancer 1,345 individuals (Framingham) NR 13q33.1
3p22.2
5q14.3
6p12.2
3q24		 Intergenic
CTDSPL
HAPLN1
PKHD1
Intergenic		 rs1529276-?
rs9311171-?
rs4466137-?
rs10498792-?
rs345013-?		 NR
NR
NR
NR
NR		 2 x 10-6
2 x 10-6
3 x 10-6
3 x 10-6
5 x 10-6 		NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Newton-Cheh
September 19, 2007
BMC Med Genet
Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study. 		Electrocardiographic traits 548-1,175 individuals, depending on measure (Framingham) NR 2q22.1
13q12.2		 Intergenic
RPL21		 rs882300-?
rs10507380-?		 NR
NR		 3 x 10-7 (PR interval)
8 x 10-6 (QT interval)		 NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Heart rate variability traits 548-1,175 individuals, depending on measure (Framingham) NR 4q34
13q13.3		 NEIL3
DCAMKL1		 rs1395479-?
rs9315385-?		 NR
NR		 7 x 10-6 (LF/HF)
8 x 10-6 (total power)		 NR
NR		 Affymetrix
[70,897]		 N
11/25/08 O'Donnell
September 19, 2007
BMC Med Genet
Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study. 		Coronary artery calcification 673-984 individuals, depending on measure (Framingham) NR 1p22.2
14q24.2
12q23.2		 Intergenic
NUMB
DRIM		 rs2390582-?
rs10483853-?
rs10507130-?		 NR
NR
NR		 1 x 10-6
6 x 10-6
7 x 10-6 		NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Subclinical atherosclerosis traits (other) 673-984 individuals, depending on measure (Framingham) NR 2q33.2
10q11.22
5p15.2
1q31.1
5p15.2
4q28.1
11q14.3
5p15.2		 ABI2
LRRC18
DNAH5
Intergenic
DNAH5
Intergenic
Intergenic
DNAH5		 rs1376877-?
rs3849150-?
rs2896103-?
rs1400544-?
rs7715811-?
rs1320267-?
rs1350445-?
rs1502050-?		 NR
NR
NR
NR
NR
NR
NR
NR		 4 x 10-7 (ICA IMT)
2 x 10-6 (AAC)
5 x 10-6 (ABI)
6 x 10-6 (CCA IMT)
6 x 10-6 (ABI)
7 x 10-6 (ABI)
9 x 10-6 (ABI)
9 x 10-6 (ABI)		 NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Seshadri
September 19, 2007
BMC Med Genet
Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. 		Cognitive test performance 705 individuals (Framingham) NR 1p22.2
21q21.3
4q13.2
6p23
14q22.1
12q23.3
5q32
11q14.1
17q22
11q25
1q42.2
12p11.1
9q22.2
2q22.1		 Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
POLR3B, RFX4
Intergenic
Intergenic
PPM1E
NCAPD3
TARBP1
Intergenic
DIRAS2
Intergenic		 rs2179965-?
rs2832077-?
rs1155865-?
rs6914079-?
rs2352904-?
rs3891355-?
rs9325032-?
rs530965-?
rs9303401-?
rs1031381-?
rs10489896-?
rs9300212-?
rs1831521-?
rs934299-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-6 (F3)
2 x 10-6 (F3)
2 x 10-6 (Nam)
2 x 10-6 (F2)
2 x 10-6 (F2)
3 x 10-6 (Sim)
3 x 10-6 (F2)
4 x 10-6 (Nam)
5 x 10-6 (NAM)
6 x 10-6 (F3)
6 x 10-6 (F2)
8 x 10-6 (WRAT)
8 x 10-6 (Nam)
9 x 10-6 (F3)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Volumetric brain MRI 705 individuals (Framingham) NR 20q13.33
11p13
11q23.2
11q22.1
4q31.3		 CDH4
EHF
NNMT
CNTN5
Intergenic		 rs1970546-?
rs5028798-?
rs2847476-?
rs952700-?
rs360929-?		 NR
NR
NR
NR
NR		 4 x 10-8 (ATCBV)
3 x 10-6 (ATBV)
3 x 10-6 (ALLV)
6 x 10-6 (AFBV)
9 x 10-6 (ALTHBV)		 NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Vasan
September 19, 2007
BMC Med Genet
Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study. 		Echocardiographic traits 1,238 individuals (Framingham) NR 4p15.31
6q15
4p15.31
8q13.3
1q31.1
2q36.1
1p31.3
5q14.3		 SLIT2
SPACA1
SLIT2
KCNB2
FAM5C
Intergenic
PDE4B
Intergenic		 rs1379659-?
rs366676-?
rs666088-?
rs10504543-?
rs1935881-?
rs10498091-?
rs10493389-?
rs4920799-?		 NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-7 (LVDD)
2 x 10-6 (LVFS)
5 x 10-6 (LVDD)
5 x 10-6 (LVSD)
6 x 10-6 (LAD)
6 x 10-6 (LVM)
7 x 10-6 (LAD)
7 x 10-6 (LVDD)		 NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Endothelial function traits 1,238 individuals (Framingham) NR 10q24.33 OBFC1 rs3814219-? NR 9 x 10-7 (BABF) NR Affymetrix
[70,897]		 N
11/25/08 " Exercise treadmill test traits 1,238 individuals (Framingham) NR 4q25
1q43
11q22.3
8p12		 NOLA1
RYR2
Intergenic
WRN		 rs6847149-?
rs2819770-?
rs746463-?
rs2553268-?		 NR
NR
NR
NR		 3 x 10-6 (S2EHR)
4 x 10-6 (S2EHR)
5 x 10-6 (P3MRSBP)
6 x 10-6 (S2ESBP)		 NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Wilk
September 19, 2007
BMC Med Genet
Framingham Heart Study genome-wide association: results for pulmonary function measures. 		Mean forced vital capacity from 2 exams 1,097-1,222 individuals, depending on measure (Framingham) NR 7q21.3
4q25		 COL1A2
Intergenic		 rs441051-?
rs10516541-?		 NR
NR		 2 x 10-6 (meanFVC)
4 x 10-6 (meanFVC)		 NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Pulmonary function traits (other) 1,097-1,222 individuals, depending on measure (Framingham) NR 15q11.2
21q22.3
15q26.1
2q36.3
8q11.22
14q22.1
14q23.1
1q21.3
17p12
7q34		 SNRPN
ADARB1
FLJ32831
RHBDD1
SNTG1
NID2
Intergenic
IL6R
CDRT4
Intergenic		 rs3867498-?
rs2838815-?
rs1455782-?
rs3820928-?
rs310558-?
rs730532-?
rs808225-?
rs4129267-?
rs2906966-?
rs357394-?		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 1 x 10-6 (FEV1slope)
3 x 10-6 (meanratio)
4 x 10-6 (ppFVC)
5 x 10-6 (ppFEV1)
5 x 10-6 (ppratio)
6 x 10-6 (ppFEF)
7 x 10-6 (ppfefrat)
7 x 10-6 (ppFEF)
8 x 10-6 (ppFEV1)
9 x 10-6 (ppFVC)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Yang
September 19, 2007
BMC Med Genet
Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study. 		Factor VII 1,000 individuals (Framingham) NR 13q34
7p22.2
1p36.32
3p26.1		 MCF2L, AB116074, AK092739, AK123267, AB002360, F7, CR603372, F10, PROZ
Intergenic
Intergenic
Intergenic		 rs561241-?
rs10488360-?
rs966321-?
rs4591494-?		 0.12
0.30
0.47
0.19		 5 x 10-16
7 x 10-6
8 x 10-6
9 x 10-6 		NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 " Hemostatic factors and hematological phenotypes 1,000 individuals (Framingham NR 11q11
14q21.3
1q23.2
2p16.2
1p31.1
8q24.13
5q21.3
11q24.1
1p34.3
12q14.2
4p15.33
10p11.21
14q32.2
20p12.3
2p16.2
5q21.1
6q25.1
6q25.1		 OR5AP2, OR5AR1, OR9G1, OR9G4
MAMDC1
OR10J1,OR10J5
Intergenic
NEGR1
Intergenic
Intergenic
Intergenic
FLJ11730, BC016328
Intergenic
Intergenic
ANKRD30A
Intergenic
Intergenic
Intergenic
Intergenic
Intergenic
MAP3K7IP2		 rs1397048-?
rs7159841-?
rs4133289-?
rs1160297-?
rs10493485-?
rs7844723-?
rs4460176-?
rs565229-?
rs9253-?
rs10506458-?
rs10489087-?
rs1200821-?
rs10484128-?
rs6108011-?
rs2357013-?
rs1829883-?
rs636864-?
rs727979-?		 0.4
0.21
0.19
0.43
0.29
0.45
0.29
0.10
0.18
0.13
0.13
0.47
0.15
0.28
0.45
0.41
0.21
0.14		 7 x 10-8 (MCH)
2 x 10-7 (Viscosity)
2 x 10-7 (Hgb)
1 x 10-6 (Hgb)
2 x 10-6 (tPA)
2 x 10-6 (Hgb)
3 x 10-6 (PAI-1)
4 x 10-6 (pltcoll)
4 x 10-6 (RBCC)
5 x 10-6 (pltcoll)
5 x 10-6 (RBCC)
6 x 10-6 (MCH)
6 x 10-6 (pltadp)
6 x 10-6 (RBCC)
6 x 10-6 (Hgb)
6 x 10-6 (MCH)
6 x 10-6 (RBCC)
8 x 10-6 (RBCC)		 NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR
NR		 Affymetrix
[70,897]		 N
11/25/08 Florez
September 10, 2007
Diabetes
A 100K genome-wide association scan for diabetes and related traits in the Framingham Heart Study: replication and integration with other genome-wide datasets 		Type 2 diabetes and 6 quantitative traits 1,087 family members 1,465 unrelated individuals; 2,175 cases and 2,412 controls NS NS NS NS NS NS Affymetrix
[66,543]		 N
11/25/08 Hanson
September 10, 2007
Diabetes
A search for variants associated with young-onset type 2 diabetes in American Indians in a 100K genotyping array 		Type 2 diabetes 300 cases, 334 controls, 121 nondiabetic siblings, 140 diabetic siblings 1,207 cases, 1,627 controls NS NS NS NS NS NS Affymetrix
[80,044]		 N
11/25/08 Hayes
September 10, 2007
Diabetes
Identification of type 2 diabetes genes in Mexican Americans through genome-wide association studies 		Type 2 diabetes 281 cases, 280 controls ~1,979 cases, ~3,092 controls NS NS NS NS NS NS Affymetrix
[88,142]		 N
11/25/08 Rampersaud
September 10, 2007
Diabetes
Identification of novel candidate genes for type 2 diabetes from a genome-wide association scan in the Old Order Amish: evidence for replication from diabetes-related quantitative traits and from independent populations 		Type 2 diabetes 124 cases, 295 controls 2,142 cases, 2,117 controls NS NS NS NS NS NS Affymetrix
[82,485]		 N
11/25/08 van Es
September 07, 2007
Lancet Neurol
ITPR2 as a susceptibility gene in sporadic amyotrophic lateral sclerosis: a genome-wide association study. 		Amyotrophic lateral sclerosis 737 cases, 721 controls 1,030 cases, 1,195 controls 12p11.23 ITPR2 rs2306677-? 0.07 3 x 10-6 1.58 [1.30-1.91] Illumina
[311,946]		 N
11/25/08 Plenge
September 05, 2007
N Engl J Med
TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. 		Rheumatoid arthritis 1,493 cases, 1,831 controls 1,053 cases, 1,858 controls 6p21.32
9q34
1p13.2		 HLA-DRB1
TRAF1-C5
PTPN22		 rs660895-?
rs3761847-G
rs2476601-?		 0.21
0.41
0.10		 1 x 10-108
4 x 10-14
2 x 10-11 		3.62 [NR]
1.32 [1.23-1.42]
1.72 [NR]		 Illumina
[297,086]		 N
11/25/08 Raelson
September 05, 2007
Proc Natl Acad Sci U S A
Genome-wide association study for Crohn's disease in the Quebec Founder Population identifies multiple validated disease loci. 		Crohn's disease 382 trios 750 cases, 828 controls, 521 trios 16q12.1
1p31.3
1p31.3		 NOD2
IL23R
IL23R		 rs5743289-?
17 marker haplotype-1
17 marker haplotype-2		 NR
0.23
0.97		 6 x 10-17
1 x 10-8
2 x 10-7 		NR
1.38 [1.23-1.53]
2.56 [1.75-3.70]		 Perlegen
[164,279]		 N
11/25/08 Menzel
September 02, 2007
Nat Genet
A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15. 		F-cell distribution 179 adults in upper and lower 5% 90 adults 11p15.5
6q23.3
2p16.1		 HBB
Intergenic
BCL11A		 NR
rs9399137-?
rs1427407-?		 0.33
0.23
0.14		 2 x 10-38
3 x 10-36
6 x 10-31 		10.2 [NR] % of variance explained
15.8 [NR] % of variance explained
13.1 [NR] % of variance explained		 Illumina
[308,015]		 N
11/25/08 Weedon
September 02, 2007
Nat Genet
A common variant of HMGA2 is associated with adult and childhood height in the general population. 		Height 4,921 individuals 29,098 individuals (19,064 adults) 12q14.3 HMGA2 rs1042725-C 0.51 6 x 10-16 .4 [NR] cm per copy in adult height Affymetrix
[364,301]		 N
11/25/08 Thorleifsson
August 09, 2007
Science
Common sequence variants in the LOXL1 gene confer susceptibility to exfoliation glaucoma. 		Glaucoma (exfoliation) 75 cases, 14,474 controls 254 cases, 198 controls 15q24.1 LOXL1 rs3825942-G 0.85 3 x 10-21 20.1 [10.80-37.41] Illumina
[304,250]		 N
11/25/08 Franke
August 08, 2007
PLoS One
Systematic association mapping identifies NELL1 as a novel IBD disease gene. 		Crohn's disease 393 cases, 399 controls 1,248 trios, 2,920 cases, 1,961 controls 16q12.1
5p13.1
11p15.1		 CARD15
PTGER4
NELL1		 rs2076756-?
rs1992660-?
rs1793004-?		 0.27
0.39
0.27		 1 x 10-21
4 x 10-7
3 x 10-6 		1.71 [1.42-2.05]
1.42 [1.24-1.67]
1.3 [1.12-1.52]		 Affymetrix
[92,387]		 N
11/25/08 Dunckley
August 01, 2007
N Engl J Med
Whole-genome analysis of sporadic amyotrophic lateral sclerosis 		Amyotrophic lateral sclerosis 386 cases, 542 controls 901 cases, 1,025 controls NS NS NS NS NS NS Affymetrix and Illumina
[776,955]		 N
11/25/08 Maeda
August 01, 2007
Kidney Int Suppl
Genetic variations associated with diabetic nephropathy and type II diabetes in a Japanese population. 		Diabetic nephropathy 94 cases, 94 controls NR 7p14.2 ELMO1 rs741301-? NR 8 x 10-6 2.67 [1.71-4.16] NR
[~80,000]		 N
11/25/08 Shifman
July 31, 2007
Mol Psychiatry
A whole genome association study of neuroticism using DNA pooling. 		Neuroticism 1,038 cases, 1,016 controls 831 cases, 702 controls 5q11.2 PDE4D rs702543-A 0.55 2 x 10-6 1.27 [1.15-1.40] Affymetrix
[452,574] (pooled)		 N
11/25/08 Hafler
July 29, 2007
N Engl J Med
Risk alleles for multiple sclerosis identified by a genomewide study. 		Multiple sclerosis 931 trios, 2,431 controls 609 trios, 2,322 cases, 2,987 controls 6p21.32
10p15.1
5p13.2
16p13.13
9q33
1p22.1		 HLA-DRA
IL2RA
IL7RA
KIAA0350
DBC1
RPL5		 rs3135388-A
rs12722489-C
rs6897932-C
rs6498169-G
rs10984447-A
rs6604026-C		 0.23
0.85
0.75
0.37
0.77
0.29		 9 x 10-81
3 x 10-8
3 x 10-7
4 x 10-6
8 x 10-6
8 x 10-6 		1.99 [1.84-2.15]
1.25 [1.11-1.36]
1.18 [1.11-1.26]
1.14 [1.08-1.21]
1.17 [1.09-1.25]
1.15 [1.08-1.22]		 Affymetrix
[334,923]		 N
11/25/08 Moffatt
July 26, 2007
Nature
Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. 		Asthma 994 cases, 1,243 controls 2,320 cases, 3,301 controls 17q12 ORMDL3 rs7216389-T 0.52 9 x 10-11 1.45 [1.17-1.81] Illumina
[307,328]		 N
11/25/08 Scuteri
July 20, 2007
PLoS Genet
Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. 		Obesity-related traits 4,741 individuals 3,205 individuals 16q12.2
16q12.2
16q12.2		 FTO
FTO
FTO		 rs9930506-A
rs9930506-A
rs9930506-A		 0.54
0.54
0.54		 3 x 10-8 (hip)
9 x 10-7 (weight)
9 x 10-7 (BMI)		 .16 [NR] SD lower (hip)
.12 [NR] SD lower (weight)
.13 [NR] SD lower (BMI)		 Affymetrix
[362,129]		 N
11/25/08 Fellay
July 19, 2007
Science
A whole-genome association study of major determinants for host control of HIV-1 		HIV1 viral setpoint 486 patients 140 patients NS NS NS NS NS NS Illumina
[535,101]		 N
11/25/08 Stefansson
July 19, 2007
N Engl J Med
A genetic risk factor for periodic limb movements in sleep. 		Restless legs syndrome 306 cases, 15,664 controls 311 cases, 1,895 controls 6p21.2 BTBD9 rs3923809-A 0.66 1 x 10-17 1.9 [1.50-2.20] Illumina
[306,937]		 N
11/25/08 Samani
July 18, 2007
N Engl J Med
Genomewide association analysis of coronary artery disease. 		Coronary disease 1,926 cases, 2,938 controls 875 cases, 1,644 controls 9p21.3
1p13.3
6q25.1
10q11.21
15q22.33
2q36.3
1q41		 Intergenic
PSRC1
MTHFD1L
CXCL12
SMAD3
pseudogene
MIA3		 rs1333049-C
rs599839-A
rs6922269-A
rs501120-T
rs17228212-C
rs2943634-C
rs17465637-C		 0.47
0.77
0.25
0.87
0.30
0.65
0.71		 3 x 10-19
4 x 10-9
3 x 10-8
9 x 10-8
2 x 10-7
2 x 10-7
1 x 10-6 		1.36 [1.27-1.46]
1.29 [1.18-1.40]
1.23 [1.15-1.33]
1.33 [1.20-1.48]
1.21 [1.13-1.30]
1.21 [1.13-1.30]
1.2 [1.12-1.30]		 Affymetrix
[377,857]		 N
11/25/08 Winkelmann
July 18, 2007
Nat Genet
Genome-wide association study of restless legs syndrome identifies common variants in three genomic regions. 		Restless legs syndrome 401 cases, 1,644 controls 1,158 cases, 1,178 controls 2p14
6p21.2
15q23		 MEIS1
BTBD9
MAP2K5, LBXCOR1		 rs2300478-G
rs9296249-T
rs12593813-G		 0.24
0.76
0.67		 3 x 10-28
4 x 10-18
1 x 10-15 		1.74 [1.57-1.92]
1.67 [1.49-1.89]
1.5 [1.36-1.66]		 Affymetrix
[236,758]		 N
11/25/08 Buch
July 15, 2007
Nat Genet
A genome-wide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease. 		Gallstones 280 cases, 360 controls 2,000 cases, 1,202 controls 2p21 ABCG8 rs11887534-C 0.10 1 x 10-14 2.2 [1.80-2.60] Affymetrix
[382,492]		 N
11/25/08 Hakonarson
July 15, 2007
Nature
A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene 		Type 1 diabetes 467 trios, 561 cases, 1,143 controls 2,350 individuals in 549 families; 390 trios 6p21.32
16p13.13
11p15.5
1p13.2		 HLA-DRB1
KIAA0350
INS
PTPN22		 rs2647044-A
rs2903692-G
rs1004446-C
rs2476601-A		 0.13
0.62
0.65
0.09		 1 x 10-16
7 x 10-11
4 x 10-9
1 x 10-7 		8.3 [6.97-9.89]
1.54 [1.32-1.79]
1.61 [1.37-1.89]
1.8 [1.44-2.24]		 Illumina
[543,071]		 N
11/25/08 Tomlinson
July 08, 2007
Nat Genet
A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. 		Colorectal cancer 930 cases, 960 controls 7,334 cases, 5,246 controls 8q24.21 Intergenic rs6983267-G 0.49 1 x 10-14 1.27 [1.16-1.39] Illumina
[547,647]		 N
11/25/08 Zanke
July 08, 2007
Nat Genet
Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. 		Colorectal cancer 1,257 cases, 1,336 controls 6,223 cases, 6,443 controls 8q24.21 ORF DQ515897 rs10505477-A 0.50 3 x 10-11 1.17 [1.12-1.23] Illumina and Affymetrix
[99,632]		 N
11/25/08 Gudbjartsson
July 01, 2007
Nature
Variants conferring risk of atrial fibrillation on chromosome 4q25. 		Atrial fibrillation/atrial flutter 550 cases, 4,476 controls 3,363 cases, 17,616 controls 4q25
4q25		 PITX2,ENPEP
PITX2,ENPEP		 rs2200733-T
rs10033464-T		 0.11
0.08		 3 x 10-41
7 x 10-11 		1.72 [1.59-1.86]
1.39 [1.26-1.53]		 Illumina
[316,515]		 N
11/25/08 Gudmundsson
July 01, 2007
Nat Genet
Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. 		Prostate cancer 1,501 cases, 11,290 controls 1,992 cases, 3,058 controls 17q12
17q24.3		 TCF2
Intergenic		 rs4430796-A
rs1859962-G		 0.49
0.46		 1 x 10-11
3 x 10-10 		1.22 [1.15-1.30]
1.2 [1.14-1.27]		 Illumina
[310,520]		 N
11/25/08 Salonen
June 26, 2007
Am J Hum Genet
Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium. 		Type 2 diabetes 500 cases, 497 controls 2,573 cases, 2,776 controls 10q25.2
2q12.1		 TCF7L2
Intergenic		 rs7903146-A
rs6712932-?		 NR
NR		 5 x 10-8
6 x 10-6 		1.71 [1.41-2.08]
1.52 [1.27-1.82]		 Illumina
[315,917]		 N
11/25/08 van Heel
June 10, 2007
Nat Genet
A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. 		Celiac disease 778 cases, 1,422 controls 991 cases, 1,489 controls 6p21.32
4q27		 HLA-DQA1
KIAA1109,TENR,IL2,IL21		 rs2187668-A
rs6822844-G		 0.14
0.82		 1 x 10-19
1 x 10-14 		7.04 [6.08-8.15]
1.59 [1.41-1.75]		 Illumina
[310,605]		 N
11/25/08 Reiman
June 07, 2007
Neuron
GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers. 		Alzheimer's disease (late onset) 446 cases, 290 controls 415 cases, 260 controls 11q14.1 GAB2 rs2373115-G 0.70 1 x 10-10 4.06 [2.81-14.69] Affymetrix
[312,316]		 N
11/25/08 WTCCC
June 07, 2007
Nature
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. 		Bipolar disorder 1,868 cases, 2,938 controls NR 16p12.1
6p21
3q27
14q23.1
20p13
2q37.3
14q32.33		 PALB2,NDUFAB1,DCTN5
NR
NR
NR
NR
NR
NR		 rs420259-A
rs6458307-?
rs683395-G
rs10134944-T
rs3761218-C
rs2953145-C
rs11622475-C		 0.72
0.69
0.08
0.09
0.64
0.23
0.70		 6 x 10-8
4 x 10-6
5 x 10-6
7 x 10-6
7 x 10-6
7 x 10-6
8 x 10-6 		2.08 [1.60-2.71]
1.19 [1.04-1.33]
1.47 [1.26-1.71]
1.45 [1.24-1.68]
1.03 [1.15-1.23]
1.84 [1.31-2.58]
1.13 [0.89-1.44]		 Affymetrix
[469,557]		 N
11/25/08 " Coronary disease 1,926 cases, 2,938 controls (see Samani 2007) 9p21.3
1q43
22q12.1
16q23.3		 CDKN2A,CDKN2B
Intergenic
Intergenic
Intergenic		 rs1333049-C
rs17672135-T
rs688034-T
rs8055236-G		 0.47
0.87
0.31
0.80		 1 x 10-13
2 x 10-6
4 x 10-6
6 x 10-6 		1.47 [1.27-1.70]
1.43 [1.23-1.64]
1.11 [0.99-1.25]
1.91 [1.33-2.74]		 Affymetrix
[469,557]		 N
11/25/08 " Crohn's disease 1,748 cases, 2,938 controls (see Parkes 2007) 2q37.1
5p13.1
1p31.3
16q12.1
3p21.31
10q24.2
18p11.21
5q33.1
10q21.2
6p21
5q31.1
7q36.1
10p15.1		 ATG16L1
Intergenic
IL23R
NOD2
BSN, MST1
NKX2-3
PTPN2
IRGM
Intergenic
NR
Intergenic
NR
NR		 rs10210302-T
rs17234657-G
rs11805303-T
rs17221417-G
rs9858542-A
rs10883365-G
rs2542151-G
rs1000113-T
rs10761659-G
rs9469220-A
rs6596075-C
rs7807268-G
rs6601764-C		 0.48
0.13
0.32
0.29
0.28
0.48
0.16
0.07
0.46
0.48
0.17
0.46
0.41		 5 x 10-14
2 x 10-12
6 x 10-12
4 x 10-11
4 x 10-8
6 x 10-8
2 x 10-7
3 x 10-7
2 x 10-6
2 x 10-6
3 x 10-6
4 x 10-6
9 x 10-6 		1.19 [1.01-1.41]
1.54 [1.34-1.76]
1.39 [1.22-1.58]
1.29 [1.13-1.46]
1.09 [0.96-1.24]
1.2 [1.03-1.39]
1.3 [1.14-1.48]
1.54 [1.31-1.82]
1.23 [1.05-1.45]
1.14 [0.98-1.32]
1.55 [1.00-2.39]
1.38 [1.20-1.60]
1.16 [1.01-1.33]		 Affymetrix
[469,557]		 N
11/25/08 " Hypertension 1,952 cases, 2,938 controls NR 1q43
15q26.2		 RYR2,CHRM3,ZP4
Intergenic		 rs2820037-T
rs2398162-A		 0.14
0.74		 8 x 10-7
6 x 10-6 		1.54 [1.03-2.31]
1.31 [1.03-1.67]		 Affymetrix
[469,557]		 N
11/25/08 " Rheumatoid arthritis 1,860 cases, 2,938 controls NR 6p21.32
6p21.32
1p13.2
7q32.3
22q12.3
21q22.3
4p15.2		 MHC
HLA-DRB1
PTPN22
Intergenic
NR
NR
NR		 rs6457617-T
rs615672-?
rs6679677-A
rs11761231-C
rs743777-G
rs2837960-G
rs3816587-C		 0.49
NR
0.10
0.62
0.29
0.17
0.41		 5 x 10-75
8 x 10-27
6 x 10-25
4 x 10-7 (sex-differentiated)
1 x 10-6
2 x 10-6
9 x 10-6 		2.36 [1.97-2.84]
NR
1.98 [1.72-2.27]
1.32 [NR] (women)
1.09 [0.97-1.24]
1.05 [0.93-1.20]
1.09 [0.96-1.25]		 Affymetrix
[469,557]		 N
11/25/08 " Type 1 diabetes 1,963 cases, 2,938 controls (see Todd 2007) 6p21.32
1p13.2
12q24.13
12q13.2
12p13.31
16p13.13
12p13.31
4q27
4q27
5q31.1		 MHC
PTPN11
SH2B3,LNK,TRAFD1,PTPN1
ERBB3
NR
KIAA0350
NR
NR
NR
NR		 rs9272346-G
rs6679677-A
rs17696736-G
rs11171739-C
rs3764021-C
rs12708716-A
rs11052552-G
rs6534347-A
rs17388568-A
rs17166496-G		 0.61
0.10
0.42
0.42
0.47
0.65
0.49
0.35
0.26
0.61		 5 x 10-134
5 x 10-26
2 x 10-14
1 x 10-11
5 x 10-8
5 x 10-7
7 x 10-7
2 x 10-6
3 x 10-6
5 x 10-6 		5.49 [4.83-6.24]
1.82 [1.59-2.09]
1.34 [1.16-1.53]
1.34 [1.17-1.54]
1.57 [1.38-1.79]
1.19 [0.97-1.45]
1.49 [1.28-1.73]
1.3 [1.10-1.55]
1.26 [1.11-1.42]
1.3 [1.15-1.47]		 Affymetrix
[469,557]		 N
11/25/08 " Type 2 diabetes 1,924 cases, 2,938 controls (see Zeggini 2007) 10q25.2
16q12.2
6p22.3
3p14
12q13.13
12q21.1
4q27		 TCF7L2
FTO
CDKAL1
NR
NR
NR
NR		 rs4506565-T
rs9939609-A
rs9465871-C
rs358806-?
rs12304921-G
rs1495377-G
rs7659604-T		 0.32
0.40
0.18
0.80
0.15
0.50
0.38		 5 x 10-12
2 x 10-7
3 x 10-7
3 x 10-6
7 x 10-6
7 x 10-6
9 x 10-6 		1.36 [1.20-1.54]
1.34 [1.17-1.52]
1.18 [1.04-1.34]
1.16 [1.03-1.33]
2.5 [1.53-4.09]
1.28 [1.11-1.49]
1.35 [1.19-1.54]		 Affymetrix
[469,557]		 N
11/25/08 Parkes
June 06, 2007
Nat Genet
Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. 		Crohn's disease 1,748 cases, 2,938 controls 1,182 cases, 2,024 controls 5p13.1
5q33.1
10q24.2
18p11.21
1q31.2
3p21.31
1q24.3
21q22.2
5q33.3		 Intergenic
IRGM
NKX2-3
PTPN2
Intergenic
MST1
Intergenic
Intergenic
IL12B		 rs9292777-?
rs13361189-?
rs10883365-?
rs2542151-?
rs10801047-?
rs9858542-?
rs12035082-?
rs2836754-?
rs6887695-?		 0.40
0.08
0.48
0.18
0.08
0.29
0.40
0.35
0.32		 3 x 10-18
2 x 10-10
4 x 10-10
3 x 10-8
3 x 10-8
5 x 10-8
2 x 10-7
5 x 10-7
9 x 10-6 		1.34 [1.20-1.50]
1.38 [1.15-1.66]
1.18 [1.05-1.32]
1.15 [1.00-1.32]
1.47 [1.22-1.76]
1.17 [1.14-1.31]
1.14 [1.02-1.27]
1.15 [1.03-1.28]
1.26 [1.12-1.41]		 see WTCCC N
11/25/08 Todd
June 06, 2007
Nat Genet
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. 		Type 1 diabetes 1,963 cases, 2,938 controls 2997 trios, 4,000 cases, 5,000 controls 1p13.2
1p13.2
12q13.2
16p13.13
12q24.13
18p11.21
2q24.2
18q22.2
11p15.5
2q11.2
5p13.2
5p13.2		 PTPN22
PHTF1, PTPN22
ERBB3
KIAA0350
C12orf30
PTPN2
IFIH1
CD226
INS
AFF3, LOC150577
CAPSL
IL7R		 rs2476601-T
rs6679677-A
rs2292239-A
rs12708716-A
rs17696736-G
rs2542151-C
rs1990760-A
rs763361-A
rs3741208-T
rs9653442-G
rs1445898-G
rs6897932-G		 0.09
0.10
0.34
0.68
0.42
0.16
0.60
0.47
0.38
0.46
0.55
0.71		 2 x 10-80
8 x 10-24
2 x 10-20
3 x 10-18
2 x 10-16
1 x 10-14
2 x 10-11
1 x 10-8
2 x 10-7
5 x 10-6
8 x 10-6
8 x 10-6 		1.98 [1.82-2.15]
1.89 [1.67-2.13]
1.28 [1.21-1.35]
1.23 [1.16-1.30]
1.22 [1.15-1.28]
1.3 [1.22-1.40]
1.18 [1.11-1.23]
1.16 [1.10-1.22]
1.25 [1.15-1.35]
1.11 [1.05-1.17]
1.12 [1.06-1.19]
1.12 [1.06-1.19]		 see WTCCC N
11/25/08 Easton
May 27, 2007
Nature
Genome-wide association study identifies novel breast cancer susceptibility loci. 		Breast cancer 390 cases, 364 controls 26,646 cases, 24,889 controls 10q26.13
16q12.1
5q11.2
8q24.21
11p15.5
5p12		 FGFR2
TNRC9, LOC643714
MAP3K1
Intergenic
LSP1
Intergenic		 rs2981582-G
rs3803662-T
rs889312-A
rs13281615-T
rs3817198-C
rs981782-C		 0.38
0.25
0.28
0.40
0.30
0.53		 2 x 10-76
1 x 10-36
7 x 10-20
5 x 10-12
3 x 10-9
9 x 10-6 		1.26 [1.23-1.30]
1.2 [1.16-1.24]
1.13 [1.10-1.16]
1.08 [1.05-1.11]
1.07 [1.04-1.11]
1.04 [1.01-1.08]		 Perlegen
[205,586]		 N
11/25/08 Hunter
May 27, 2007
Nat Genet
A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. 		Breast cancer 1,145 cases, 1,142 controls 1,176 cases, 2,072 controls 10q26.13 FGFR2 rs1219648-G 0.40 1 x 10-10 1.2 [1.07-1.42] Illumina
[528,173]		 N
11/25/08 Stacey
May 27, 2007
Nat Genet
Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. 		Breast cancer 1,599 cases, 11,546 controls 2,934 cases, 5,967 controls 16q12.1
2q35		 TNRC9
Intergenic		 rs3803662-T
rs13387042-A		 0.27
0.50		 6 x 10-19
1 x 10-13 		1.28 [1.21-1.35]
1.2 [1.14-1.26]		 Illumina
[311,524]		 N
11/25/08 Kindmark
May 15, 2007
Pharmacogenomics J
Genome-wide pharmacogenetic investigation of a hepatic adverse event without clinical signs of immunopathology suggests an underlying immune pathogenesis 		Response to ximelagatran treatment 74 cases, 130 controls 10 cases, 16 controls 6p21.3 HLA-DRB1 DRB1*07 NR 9 x 10-6 4.41 [2.20-8.87] Perlegen
[~266,722]		 N
11/25/08 Baum
May 08, 2007
Mol Psychiatry
A genome-wide association study implicates diacylglycerol kinase eta (DGKH) and several other genes in the etiology of bipolar disorder. 		Bipolar disorder 461 cases, 563 controls 772 cases, 876 controls 13q14.11 DGKH rs1012053-A 0.84 2 x 10-8 1.59 [1.35-1.87] Illumina
[555,235] (pooled)		 N
11/25/08 Matarin
May 06, 2007
Lancet Neurol
A genome-wide genotyping study in patients with ischaemic stroke: initial analysis and data release. 		Stroke 259 cases, 269 controls NR 18p11.21
13q21.1
7p21
6q21		 IMPA2
Intergenic
Intergenic
AIM1		 rs7506045-?
rs9536591-?
rs10486776-?
rs783396-?		 0.10
0.10
0.10
0.90		 7 x 10-7
6 x 10-6
6 x 10-6
9 x 10-6 		5.39 [2.77-10.5]
1.92 [1.41-2.63]
5.62 [2.66-11.9]
2.17 [1.47-3.13]		 Illumina
[408,803]		 N
11/25/08 Helgadottir
May 03, 2007
Science
A common variant on chromosome 9p21 affects the risk of myocardial infarction. 		Myocardial infarction 1,607 cases, 6,728 controls 2,980 cases, 6,309 controls 9p21.3 CDKN2A,CDKN2B rs10757278-G 0.45 1 x 10-20 1.28 [1.22-1.35] Illumina
[305,953]		 N
11/25/08 McPherson
May 03, 2007
Science
A common allele on chromosome 9 associated with coronary heart disease 		Coronary disease 322 cases, 312 controls 3,984 cases, 19,807 controls NS NS NS NS NS NS Perlegen
[72,864]		 N
11/25/08 Huentelman
April 30, 2007
Hum Mol Genet
Calmodulin-binding transcription activator 1 (CAMTA1) alleles predispose human episodic memory performance 		Episodic memory 341 young adults 472 young adults NS NS NS NS NS NS Affymetrix
[~502,627] (pooled)		 N
02/13/09 Saxena
April 26, 2007
Science
Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. 		Triglycerides up to 5,217 individuals NR 16q13
19q13.32
8p21.3
2p24.1
16q13		 CETP
APOE cluster
LPL
APOB
CETP		 rs1800775-C
rs4420638-G
rs328-T
rs693-A
rs1800775-C		 0.47
0.22
0.10
0.49
0.44		 3 x 10-13 (HDL)
3 x 10-13 (LDL)
5 x 10-7 (TG)
7 x 10-7 (LDL)
3 x 10-6 (apoA-1)		 2.1 % [NR] of variance explained
2.4 % [NR] of variance explained
1 % [NR] of variance explained
NR
1.6 % [NR] of variance explained		 Affymetrix
[386,731]		 N
11/25/08 " Type 2 diabetes 1,464 cases, 1,467 controls 5,065 cases, 5,785 controls (also includes meta-analysis from DGI+FUSION+WTCCC) 10q25.2
6p22.3
10q23.33
3q27.2
8q24.11
9p21.3
11p15.1
3p25.2		 TCF7L2
CDKAL1
HHEX
IGF2BP2
SLC30A8
CDKN2A,CDKN2B
KCNJ11
PPARG		 rs7903146-T
rs7754840-C
rs1111875-C
rs4402960-T
rs13266634-C
rs10811661-T
rs5219-T
rs1801282-C		 0.26
0.31
0.53
0.29
0.65
0.83
0.47
0.86		 2 x 10-31
4 x 10-11 (DGI+FUSION+WTCCC)
6 x 10-10 (DGI+FUSION+WTCCC)
2 x 10-9
5 x 10-8 (DGI+FUSION+WTCCC)
5 x 10-8
1 x 10-7
2 x 10-6 (DGI+FUSION+WTCCC)		 1.38 [1.31-1.46]
1.12 [1.08-1.16]
1.13 [1.08-1.17]
1.17 [1.11-1.23]
1.12 [1.07-1.16]
1.2 [1.12-1.28]
1.15 [1.09-1.21]
1.14 [1.08-1.20]		 Affymetrix
[386,731]		 N
11/25/08 Scott
April 26, 2007
Science
A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. 		Type 2 diabetes 1,161 cases, 1,174 controls 1,215 cases, 1,258 controls (also includes meta-analysis from DGI+FUSION+WTCCC) 3q27.2
9p21.3
16q12.2
6p22.3
11p15.1
10q23.33
10q25.2
8q24.11
11p12
3p25.2		 IGF2BP2
CDKN2A,CDKN2B
FTO
CDKAL1
KCNJ11
HHEX
TCF7L2
SLC30A8
Intergenic
PPARG		 rs4402960-T
rs10811661-T
rs8050136-A
rs7754840-C
rs5219-T
rs1111875-C
rs7903146-T
rs13266634-C
rs9300039-C
rs1801282-C		 0.30
0.85
0.38
0.36
0.46
0.52
0.18
0.61
0.89
0.82		 9 x 10-16 (DGI+FUSION+WTCCC)
8 x 10-15 (DGI+FUSION+WTCCC)
1 x 10-12 (DGI+FUSION+WTCCC)
4 x 10-11 (DGI+FUSION+WTCCC)
7 x 10-11 (DGI+FUSION+WTCCC)
6 x 10-10 (DGI+FUSION+WTCCC)
1 x 10-8
5 x 10-8 (DGI+FUSION+WTCCC)
6 x 10-8
2 x 10-6 (DGI+FUSION+WTCCC)		 1.14 [1.11-1.18]
1.2 [1.14-1.25]
1.17 [1.12-1.22]
1.12 [1.08-1.16]
1.14 [1.10-1.19]
1.13 [1.09-1.17]
1.34 [1.21-1.49]
1.12 [1.07-1.16]
1.48 [1.28-1.71]
1.14 [1.08-1.20]		 Illumina
[315,635]		 N
11/25/08 Steinthorsdottir
April 26, 2007
Nat Genet
A variant in CDKAL1 influences insulin response and risk of type 2 diabetes. 		Type 2 diabetes 1,399 EA cases, 5,275 EA controls 2,437 EA cases, 7,287 EA controls 10q25.2
6p22.3
8q24.11		 TCF7L2
CDKAL1
SLC30A8		 rs7903146-?
rs7756992-G
rs13266634-C		 0.30
0.26
0.67		 2 x 10-10
8 x 10-9
3 x 10-6 		1.38 [NR]
1.2 [1.13-1.27]
1.15 [1.08-1.22]		 Illumina
[313,179 SNPs; 339,846 2-SNP haplotypes]		 N
11/25/08 Zeggini
April 26, 2007
Science
Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. 		Type 2 diabetes 1,924 cases, 2,938 controls 3,757 cases, 5,346 controls (also includes meta-analysis from DGI+FUSION+WTCCC) 10q25.2
3q27.2
16q12.2
11p15.1
6p22.3
8q24.11
9p21.3
3p25.2
10q23.33
9p21.3		 TCF7L2
IGF2BP2
FTO
KCNJ11
CDKAL1
SLC30A8
CDKN2A, CDKN2B
PPARG
HHEX
CDKN2A, CDKN2B		 rs7901695-C
rs4402960-T
rs8050136-A
rs5215-C
rs10946398-C
rs13266634-C
rs564398-T
rs1801282-C
rs5015480-C
rs10811661-T		 NR
0.32
0.40
NR
0.32
0.69
0.56
NR
0.57
0.83		 1 x 10-48 (DGI+FUSION+WTCCC)
9 x 10-16 (DGI+FUSION+WTCCC)
7 x 10-14
5 x 10-11 (DGI+FUSION+WTCCC)
1 x 10-8
5 x 10-8 (DGI+FUSION+WTCCC)
1 x 10-6
2 x 10-6 (DGI+FUSION+WTCCC)
5 x 10-6
5 x 10-6 		1.37 [1.31-1.43]
1.14 [1.11-1.18]
1.23 [1.18-1.32]
1.14 [1.10-1.19]
1.16 [1.10-1.22]
1.12 [1.07-1.16]
1.13 [1.08-1.19]
1.14 [1.08-1.20]
1.13 [1.07-1.19]
1.19 [1.11-1.28]		 Affymetrix
[393,453]		 N
11/25/08 Rioux
April 15, 2007
Nat Genet
Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. 		Crohn's disease 946 cases, 977 controls 530 trios, 353 cases, 207 controls 16q12.1
2q37.1
1p31.3
10q21.2		 CARD15
ATG16L1
IL23R
Intergenic		 rs2076756-?
rs2241880-G
rs7517847-?
rs224136-?		 0.24
0.55
0.40
0.81		 7 x 10-14
1 x 10-13
3 x 10-12
1 x 10-10 		NR
1.45 [1.27-1.64]
NR
1.67 [NR]		 Illumina
[304,413]		 N
11/25/08 Frayling
April 12, 2007
Science
A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. 		Body mass index 10,657 adults 19,424 adults, 10,172 children 16q12.2 FTO rs9939609-A 0.39 2 x 10-20 .36 [NR] kg/m2 per copy in adults Affymetrix
[490,032]		 N
11/25/08 Uhl
April 03, 2007
BMC Genet
Molecular genetics of nicotine dependence and abstinence: whole genome association using 520,000 SNPs 		Nicotine dependence 134 cases, 320 controls NR NS NS NS NS NS NS Affymetrix
[~520,000] (pooled)		 N
11/25/08 Coon
April 01, 2007
J Clin Psychiatry
A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease. 		Alzheimer's disease (late onset) 664 cases, 422 controls NR 19q13.32 APOE rs4420638-? NR 1 x 10-39 4.01 [NR] Affymetrix
[~502,627]		 N
11/25/08 Gudmundsson
April 01, 2007
Nat Genet
Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. 		Prostate cancer 1,453 cases, 3,064 controls 1,210 EA cases, 2,445 EA controls; 373 AA cases, 372 AA controls 8q24.21
8q24.21
8q24.21		 Intergenic
Intergenic
Intergenic		 rs1447295-A
HapC
rs16901979-A		 0.09
0.02 (EA)
0.03 (EA)		 6 x 10-18
3 x 10-15 (EA)
1 x 10-12 (EA)		 1.6 [1.43-1.77]
2.1 [1.75-2.53] (EA)
1.79 [1.53-2.11] (EA)		 Illumina
[316,515]		 N
11/25/08 Hanson
April 01, 2007
Diabetes
Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study. 		End-stage renal disease 105 cases, 102 controls NR 8q24.21 PVT1 rs2648875-A 0.53 2 x 10-6 2.97 [1.90-4.65] Affymetrix
[115,352]		 N
11/25/08 Yeager
April 01, 2007
Nat Genet
Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. 		Prostate cancer 1,172 cases, 1,157 controls 3,124 cases, 3,142 controls 8q24.21
8q24.21		 Intergenic
Intergenic		 rs1447295-A
rs6983267-G		 0.11
0.50		 2 x 10-14
9 x 10-13 		1.43 [1.29-1.59]
1.26 [1.13-1.41]		 Illumina
[538,548]		 N
11/25/08 Lencz
March 20, 2007
Mol Psychiatry
Converging evidence for a pseudoautosomal cytokine receptor gene locus in schizophrenia. 		Schizophrenia 178 cases, 144 controls NR Xp22.33,Yp11.32 CSF2RA,IL3RA rs4129148-C NR 4 x 10-7 3.23 [2.04-5.15] Affymetrix
[439,511]		 N
11/25/08 Melquist
March 08, 2007
Am J Hum Genet
Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms 		Progressive supranuclear palsy 288 cases, 344 controls 213 cases, 391 controls NS NS NS NS NS NS Affymetrix
[428,867] (pooled)		 N
11/25/08 Libioulle
March 05, 2007
PLoS Genet
Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. 		Crohn's disease 547 cases, 928 controls 1,266 cases, 559 controls, 428 trios 1p31.3
5p13.1
16q12.1		 IL23R
Intergenic
CARD15		 rs11209026-?
rs1373692-?
rs5743289-?		 0.92
0.59
NR		 2 x 10-18
2 x 10-12
1 x 10-6 		2.92 [NR]
1.46 [NR]
NR		 Illumina
[302,451]		 N
11/25/08 Schymick
February 20, 2007
Lancet Neurol
Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. 		Amyotrophic lateral sclerosis 276 cases, 276 controls NR 10q26.2
2p24.2
8q24.2
20q13.2
9q31.3
4q31.3		 Intergenic
Intergenic
Intergenic
ZFP64
SUSD1
KIAA1727		 rs4363506-?
rs16984239-?
rs12680546-?
rs6013382-?
rs2782931-?
rs11099864-?		 NR
NR
NR
NR
NR
NR		 7 x 10-7
2 x 10-6
3 x 10-6
5 x 10-6
6 x 10-6
9 x 10-6 		1.9 [1.50-2.40]
2.1 [1.50-3.00]
1.67 [1.25-2.00]
1.43 [1.11-1.67]
1.11 [0.91-1.43]
1 [0.80-1.40]		 Illumina
[549,062]		 N
11/25/08 Sladek
February 11, 2007
Nature
A genome-wide association study identifies novel risk loci for type 2 diabetes. 		Type 2 diabetes 661 cases, 614 controls 2,617 cases, 2,894 controls 10q25.2
8q24.11
10q23.33		 TCF7L2
SLC30A8
HHEX		 rs7903146-T
rs13266634-C
rs1111875-G		 0.30
0.70
0.60		 2 x 10-34
6 x 10-8
3 x 10-6 		1.65 [1.28, 2.02]
1.18 [0.69-1.67]
1.19 [0.82-1.56]		 Illumina
[392,935]		 N
11/25/08 Spinola
January 16, 2007
Cancer Lett
Genome-wide single nucleotide polymorphism analysis of lung cancer risk detects the KLF6 gene 		Lung cancer 338 Italian lung adenocarcinoma cases, 335 Italian controls 265 Norwegian non-small lung carcinoma cases 356 Norwegian controls NS NS NS NS NS NS Affymetrix
[~116,204] (pooled)		 N
11/25/08 Bierut
December 07, 2006
Hum Mol Genet
Novel genes identified in a high-density genome wide association study for nicotine dependence. 		Nicotine dependence 1,050 cases, 879 controls NR 21q22.2
10q21.3		 NR
CTNNA3		 rs2836823-T
rs4142041-G		 0.40
0.34		 2 x 10-6
6 x 10-6 		1.46 [1.23-1.73]
1.14 [0.97-1.35]		 Perlegen
[2.4 million] (pooled)		 N
11/25/08 Liu
December 05, 2006
Am J Med Genet B Neuropsychiatr Genet
Addiction molecular genetics: 639,401 SNP whole genome association identifies many "cell adhesion" genes 		Addiction 980 cases, 680 controls NR NS NS NS NS NS NS Affymetrix
[639,401]		 N
11/25/08 Duerr
October 26, 2006
Science
A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. 		Inflammatory bowel disease 547 cases, 548 controls 401 cases, 433 controls, 883 families, 1,119 affected offspring 1p31.3
1p31.3
16q12.1		 IL23R
IL23R
CARD15		 rs7517847-C
rs11209026-G
rs2076756-?		 0.56
0.93
NR		 4 x 10-13
4 x 10-11
5 x 10-10 		1.61 [1.35-1.92]
3.84 [2.33-6.66]
NR		 Illumina
[308,332]		 N
11/25/08 Papassotiropoulos
October 20, 2006
Science
Common Kibra alleles are associated with human memory performance 		Memory performance 341 individuals 680 individuals NS NS NS NS NS NS Affymetrix
[178,390](pooled)		 N
11/25/08 DeWan
October 19, 2006
Science
HTRA1 promoter polymorphism in wet age-related macular degeneration. 		Age-related macular degeneration (wet) 96 Southeast Asian cases, 130 Southeast Asian controls NR 10q26.13 HTRA1 rs11200638-A NR 8 x 10-12 1.6 [0.71-3.61] Affymetrix
[97,824]		 N
11/25/08 Fung
September 28, 2006
Lancet Neurol
Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. 		Parkinson's disease 267 cases, 270 controls NR 10q11.21
4q13.2
11q14.1		 Intergenic
BRDG1
DLG2		 rs1480597-?
rs2242330-?
rs10501570-?		 NR
NR
NR		 2 x 10-6
2 x 10-6
7 x 10-6 		2.5 [1.67-3.33]
2 [1.43-2.50]
5 [2.00-12.50]		 Illumina
[408,803]		 N
11/25/08 Arking
April 30, 2006
Nat Genet
A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization. 		QT interval 100 > 445ms, 100 < 386ms 200 > 85th pct, 200 < 15th pct, 7,817 cohort members 1q23.3 NOS1AP rs10494366-? 0.36 1 x 10-10 4.9 - 7.90 [NR] msec difference between homozygotes Affymetrix
[88,500]		 N
11/25/08 Herbert
April 14, 2006
Science
A common genetic variant is associated with adult and childhood obesity 		Obesity 694 offspring 3,489 cases, 6,392 controls, 361 trios NS NS NS NS NS NS Affymetrix
[86,604]		 N
11/25/08 Maraganore
September 09, 2005
Am J Hum Genet
High-resolution whole-genome association study of Parkinson disease. 		Parkinson's disease 443 sib pairs 332 cases, 332 controls 5p15.2 SEMA5A rs7702187-? NR 8 x 10-6 1.74 [1.36-2.24] Perlegen
[198,345]		 N
11/25/08 Klein
March 10, 2005
Science
Complement factor H polymorphism in age-related macular degeneration. 		Age-related macular degeneration 96 cases, 50 controls NR 1q31.1 CFH rs380390-C 0.70 (HapMap CEU) 4 x 10-8 4.6 [2.0-11] Affymetrix
[103,611]		 N

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Last Updated: July 16, 2010