Haplotype: definition

The set of SNP (single nucliotide polymorphism) alleles along a region of a chromosome. Theoretically there could be many haplotypes in a chromosome region, but recent studies are typically finding only a few common haplotypes. Some SNP alleles are the actual functional variants that contribute to the risk of getting a disease. Individuals with such a SNP allele have a higher risk for that disease than do individuals without that SNP allele. Most SNPs are not these functional variants, but are useful as markers for finding them. To find the regions with genes that contribute to a disease, the frequencies of many SNP alleles are compared in individuals with and without the disease. When a particular region has SNP alleles that are more frequent in individuals with the disease than in individuals without the disease, those SNPs and their alleles are associated with the disease. These associations between a SNP and a disease indicate that there may be genes in that region that contribute to the disease.40