The second locus chosen for modeling a population specific phenotype is LCT located on chromosome 2. A variant within LCT gene, rs4988235 (C/T -13910), is associated with lactase persistence, leading to ability to digest milk in adults, and has been demonstrated to be under strong positive selection in Europeans (Bersaglieri, et al., 2004; Hamblin and Di Rienzo, 2000; Tishkoff, et al., 2007). Allele A is found at 0.75 frequency in HapMap European samples, but is absent in HapMap YRI, CHB and JPT samples. Since rs4988235 genotypes were not available for our sample set, an allele A for rs1446585, a nearby SNP in strong LD with allele T of rs4988235 (r2=0.73 in HapMap CEU samples) was used for modeling. Individuals homozygous for allele A for rs1446585 were designated as surrogate cases, while individuals with A/G and G/G genotypes were designated as surrogate controls (Allele A is 0.792 in CEU, and 0.00 in CHB, JPT, and YRI).
