In all GWAS, imputation to phased haplotype data from the founders of the CEU and YRI HapMap Phase 2 samples (build 21) was performed using MACH 1, IMPUTE22 or BEAGLE3. SNPs with lower imputation quality scores (r2<0.3) (Supplementary Table 2) as well as SNPs with a small number of allele counts after stratifying by sex and case-control status were excluded from analyses. Local ancestry, defined as the number of European chromosomes (continuous between 0–2), was estimated for the majority of the Stage 1 African ancestry studies (Supplemental Table 8), using HAPMIX4. To evaluate the effect of admixture on the allele distribution between African and European segments we stratified the analysis of each variant by local ancestry at each locus (Supplementary Table 9).
