Haplotypes were reconstructed from genotypes using PHASE. A region spanning SNPs 2 through 5 (rs933271, rs5993883, rs739368, and rs740603) of the 15-SNP haplotype was chosen as a core from which to evaluate patterns in homozygosity. This was chosen as a core because the most common 15-SNP haplotype in EAs contains the derived allele state at rs933271, rs5993883, and rs740603. The web-based Extended Haplotype Homozygosity Calculator and Plotter (Mueller and Andreoli, 2004) was used to examine the decay of homozygosity for haplotypes of the core. Sweep software (Sabeti et al., 2002) was used to calculate Relative Extended Haplotype Homozygosity (REHH).
