The surrogate phenotypes were assigned based on SNPs selected from haplotype analyses of three regions that contained genes with strong ancestry association. The models chosen were for the SLC24A5, lactase gene (LCT) and ADH1B. SLC24A5, coding for a K gated Na/Ca exchanger, is located on chromosome 15, and plays a role in human skin pigmentation (Lamason, et al., 2005). This study provided evidence that a non-synonymous genetic substitution (rs1426654, A/G 111) is under strong positive selection in Europeans, with allele A nearly fixed in various European populations (98.7 to 100%), whereas allele G is present at 97 to 100% frequency in African and East Asian HapMap populations (Lamason, et al., 2005). Since genotypes for rs1426654 was not available in our dataset, individuals homozygous for allele A of rs2675348, in complete linkage disequilibrium (LD) with allele A of rs1426654 (r2 =1.00 in HapMap CEU samples), were designated as surrogate cases, while individuals with A/G and G/G genotypes were designated as surrogate controls (Allele A is 1.0 in CEU, 0.5 in CHB, 0.589 in JPT, and 0.25 in YRI).
