SNPs from each dataset were ranked according to MAF. To construct the Illumina and Affymetrix "low frequency" SNPs, we made groups starting with the lowest frequency SNP and progressively included the next 10 SNPs. The final groups included the 1,000 SNPs with the lowest MAFs in each dataset. For the "high frequency" SNPs, we began at the SNP with the highest MAF and constructed groups in the same manner. The MAFs of the SNPs in the four 1,000 SNP sets are described in Table 1.
