Imputation was performed on an array-wise basis. We first pre-phased the genotypes with Shape-it v2.r7271948. We then imputed variants from the 1000 Genomes Project (phase I integrated release, March 2012, with Aug 2012 chromosome X update, a cosmopolitan reference panel with singletons removed) with Impute2 v2.3049–51. The estimated quality control metric rinfo2 used in this study is the info metric from Impute2, which is an estimate of the imputed genotype correlation to the true genotype52. Poorly imputed (rinfo2<0.3) and MAC<20 SNPs were removed, resulting in 24,149,855 (EUR), 20,828,585 (LAT), 15,248,462 (EAS), 21,485,958 (AFR), and 8,607,429 (SAS) SNPs (28,613,428 unique SNPs) available for analyses.
