Genomic DNAs passing quality control (QC) standards were genotyped on Affymetrix v6.0 SNP arrays. All arrays included in analysis passed standard QC measures. Genotypes were called using BEAGLECALL (Browning and Yu, 2009), followed by rigorous genotype QC. We imputed the 1000 Genomes Project (1000 Genomes Project Consortium, 2010) April 2012 integrated variant reference panel of 36.5 million simple nucleotide polymorphisms (SNPs) using IMPUTE2 (Howie et al., 2009). We converted posterior genotypic probabilities to allelic dosages using GenABEL (Aulchenko et al., 2007). After post-imputation QC, 8,344,348 SNPs were available for analysis. Complete details of array, SNP and individual QC, BEAGLECALL genotyping, imputation and post-imputation QC are included in Supplementary Information and Supplementary Figures S1–S3.
