The SNPs chosen for inclusion were based on two large sets of previous genotyping results in our laboratory (Tian, et al., 2007 (link); Tian, et al., 2006 (link)) were limited to those SNPs that overlapped with the 300K genome-wide Illumina SNP array. 250 SNPs were chosen selecting the best SNP in each 10 cM deCODE bin that met the criteria of a large allele frequency differences (>45%) between EURA and AMI groups and small allele frequency differences (<5%) between two disparate AMI groups (Pima and Mayan). Similarly, 250 SNPs with large frequency differences (>45%) between African and European groups were selected. From these 500 SNPs we reduced the number for testing to 184 based on the following criteria: 1) in silico design criteria for TaqMan assays; 2) genome-wide distribution pattern (minimum inter-marker distance = 8 cM on deCODE map); and 3) EAS differences based on HapMap results in JPT and CHB. TaqMan® SNP genotyping assays were designed for the 184 SNPs and tested using DNA panels. Of these, 128 SNPs passed our quality filters demonstrating reproducible genotyping results in population samples of diverse origin, >90% complete typing results in each population and were in HW equilibrium (p>0.01) in the EURA group. A small number of SNPs were not in HW equilibrium in specific populations (2 SNPs in AFR, 3 SNPs AMI, and 3 SNPs EAS). These SNPs did not overlap between these groups and only 2 SNPs showed HW <0.005). Thus, these SNPs were not excluded, because recent admixture in these self-identified ethnic groups could result in departure from HW. Summary information for the final set of 128 SNPs is provided in Supplementary Table S1.