Genotypes were imputed with IMPUTE2 (16) using the genotyped SNPs and the 1000 Genomes reference panel released in June 2011 (http://www.1000genomes.org/), which contains phased haplotypes for 1,094 individuals of various ancestries, including 379 samples of European descent (CEU, FIN, GBR, IBS, and TCI), 286 of Asian descent (CHB, JPT, and CHS), 181 admixed American samples (PUR, CLM, and MXL), and 246 samples of African descent (ASW, LWK, YR) (17). EA and AA samples were imputed separately. Genotyped SNPs with Hardy-Weinberg equilibrium P-values <10−5 were set to missing and imputed genotypes were used instead. We retained 18,564,419 SNPs with derived information content > 0.8 in at least one of the population groups.
