Genotyping coordinates are given in NCBI Build 36/UCSC hg18. For the discovery phase, quality control was conducted separately for each resolved sample. SNPs were removed for missingness ≥0.02, case–control difference in SNP missingness ≥0.02, SNP frequency difference from HapMap3 [ref. 50] ≥0.15, or exact Hardy–Weinberg equilibrium test in controls <1×10−6. Subjects were removed for excessive missingness (≥0.02), identical or closely related to any subject in any sample (π̂> 0.2 based on common autosomal SNPs) and if there was evidence for diverging ancestry. Ancestry was estimated using multidimensional scaling applied to 8549 SNPs directly genotyped in all samples and in approximate linkage equilibrium.
