It is important to examine not just the 11 previously identified SNPs listed in Table 1, but all SNPs correlated with these 11 SNPs in Europeans. We used a two-step process to define distinct groups of correlated SNPs, which we call bins. First, we grouped previously identified SNPs by their correlation in the 1000 Genomes Pilot 1 CEU (i.e. European ancestry) reference sample, using r2≥0.7 as our threshold [Durbin, et al. 2010]. Under this strategy, the 11 previously identified SNPs listed in Table 1 are partitioned into four groups: Group A (rs16969968, rs1051730), Group B (rs588765, rs880395), Group C (rs6495308, rs2036534, rs7163730, rs9788682, rs684513, rs578776), and Group D (rs2869046) (Table 2). From these four groups, we established the bins by including all SNPs correlated (r2≥0.7) in the European ancestry reference sample with at least one of the SNPs defining the bin. The threshold of 0.7 was chosen to provide an inclusive collection of tested SNPs. Using SNAP to obtain correlated variants in a bin based on 1000 Genomes Pilot 1 CEU, we identified 52 SNPs in bin A, 111 SNPs in bin B, 82 SNPs in bin C, and 15 SNPs in bin D.
