Genome-wide genotype imputation of SNPs and insertion/deletion polymorphisms (indels) was conducted separately by ancestry group using IMPUTE2 (Howie et al., 2011) with reference to all 1000 Genomes haplotype panels (see Supplemental Information).(Durbin et al., 2010) For each imputed SNP and indel, a dosage value (a fractional value between 0 and 2 indicating the expected number of minor allele copies) and an “info” metric (a fractional value typically between 0 and 1 with higher values indicating SNPs imputed with higher certainty) were generated. We filtered imputed SNPs and indels based on minor allele frequency (MAF)<1% in the 1000 Genomes populations of African (AFR) or European (EUR) descent, leaving 6,809,218 SNPs and 739,119 indels in the AAs and 6,727,359 SNPs and 729,634 indels in the EAs.
