Imputation of SNPs from the 1000 Genomes Project was performed using IMPUTE229 and haplotypes from all 1,092 individuals in the 1000 Genomes June 2011 Data Release30 as a reference dataset (Supplementary Methods). Post-imputation QC and allelic dosage analysis were conducted in each subpopulation separately in PLINK followed by case-weighted meta-analysis in METAL.
