For each stage 1 sample set, we imputed genotypes for autosomal SNPs that were present in HapMap Phase II but were not present in the genome-wide chip or did not pass direct genotyping QC. In each sample, genotypes were imputed using the genotype data from the GWA chips and phased HapMap II genotype data from the 60 CEU HapMap founders. We retained SNPs that had an estimated MAF>0.01 in the control samples. Imputed SNPs were then tested for T2D association. The genomic control values for these imputed SNPs were 1.08 (UK), 1.07 (DGI) and 1.04 (FUSION) (Supplementary Methods).
