SNPs with a call rate of 98% or greater in the EAs (n=1,015,550) were included and subjected to further quality control. From these, SNPs were removed if the minor allele frequency was less than 0.01 in the combined case and control dataset (n=161,048) or if among those with minor allele frequency ≥ 0.01 there was significant deviation from Hardy Weinberg equilibrium (p<10−4) in the controls (n=1,127). The final dataset for analysis of EAs consisted of 853,375 SNPs that passed all quality control measures. Similar quality control thresholds were applied to the 1,010,230 SNPs with a call rate of 98% or greater in the AAs. This resulted in removal of 68,600 SNPs with a minor allele frequency below 0.01 in the combined AA case and control sample, and 332 SNPs that demonstrated significant deviation from Hardy Weinberg equilibrium in AA controls. The final dataset for the AA sample consisted of 941,298 SNPs. Positions of all SNPs are from dbSNP build 130, genome build 36.3.
