HapMap (short for "haplotype map") is the nickname of the International HapMap Project, an international project that seeks to relate variations in human DNA sequences with genes associated with health. A haplotype is a set of DNA variations, or polymorphisms, that tend to be inherited together. A haplotype can refer to a combination of alleles or to a set of single nucleotide polymorphisms (SNPs) found on the same chromosome. The HapMap describes common patterns of genetic variation among people.
HapMap is really shorthand for "haplotype map". This was a project which was conducted in great intensity from about 2003 to 2006 to enable a determination of how it is that variation in the human genome travels in neighborhoods, and how those neighborhoods are boundaried, and how that is different between Europe and Asia, and Africa. The study involved looking at 270 DNA samples and characterizing their variation at a very high level of detail and understanding how these neighborhoods across chromosomes, some of which are as small as a thousand or so base pairs, and some of which are big as 100,000, basically allow the SNPs in that interval to travel in lock-step. This is what we call linkage disequilibrium, and the HapMap defined that across the whole genome for the first time in a way that is extremely valuable for trying to understand the relationship between variation and disease.Francis S. Collins, M.D., Ph.D.