Genetic variation refers to diversity in gene frequencies. Genetic variation can refer to differences between individuals or to differences between populations. Mutation is the ultimate source of genetic variation, but mechanisms such as sexual reproduction and genetic drift contribute to it as well.
Variation in the human genome can take several forms. Simple single nucleotide polymorphisms, or SNPs, is one form. But in another form actually involves a larger-scale variation where you might have a stretch of DNA of hundreds, or even thousands, of base pairs that is different between people. Maybe I have three copies of that stretch and you have two. Or maybe it's a circumstance where I have the genes in the order ABC and you have them in the order of ACB because you have an inversion in that. Those don't have to be pathological. In fact, most of them won't be, but it's a different kind of variation that in some instances may be playing a role in disease risk.