Figure 2.

Linkage disequilibrium and haplotypes. (A) For a C>T SNP, the minor T allele shows association with cases of disease, being present twice as often as in controls. (B) However, when further variants are genotyped, a second G>C SNP shows perfect linkage disequilibrium with the initial disease associated SNP: everyone who has the T allele of the first SNP always has the C allele of the second SNP and it is not possible to say whether the disease association is due to the first or second SNP. (C) For four SNPs there are 16 possible combinations in which they could theoretically occur together in a population. However, variants occur together more often than expected by chance and the observed coinherited blocks of variants are described as haplotypes, of which three are present in this theoretical population sample. (D) Haplotype blocks break down at sites of recombination. Understanding the haplotype block structure of the genome across populations is highly informative for population genetics studies.²⁰