first 10 PCs for each. Participants with PC scores >3 standard deviations from the mean of any of the 10 PCs were removed as outliers, leaving 209,020 EA; 57,340 AA; 14,425 LA; 1410 EAA; and 196 SAA subjects. Within genetically defined populations, we calculated population-specific imputation INFO scores using SNPTEST v2 (ref. 46) and retained SNPs with INFO scores >0.7 for association analyses. Imputed genotypes with posterior probability ≥0.9 were transferred to best guess. We removed both genotyped and imputed SNPs with genotype call rates or best guess rates ≤0.95 and HWE p value ≤ 1 × 10−6 in each population, using different MAF thresholds to filter SNPs: EA (0.0005), AA (0.001), LA (0.01), EAA (0.05), and SAA (0.05). The approximate number of SNPs remaining in each population was EA: 6.8 million, AA: 12.5 million, LA: 5.6 million, EAA: 2.6 million, and SA: 2.6 million.
