We use the term diplotype to mean a pair of two-SNP haplotypes belonging to an individual. Let represent the diplotype comprising the two haplotypes 10 and 11 (i.e. having genotype 2 at SNP A and genotype 1 at SNP B). To obtain a diplotype distribution, we assume Hardy-Weinberg equilibrium (HWE) for haplotypes, which real data tends to follow in the context we are considering. For example, . There are 10 possible diplotypes but only nine distinguishable pairs of genotypes. In particular, the genotype pair consisting of two heterozygotes can correspond to either of the two diplotypes or . We only consider analyses using genotypes so will sum over this diplotype pair where necessary.
