Participants were genotyped on the Illumina Human 1M BeadChip (San Diego, CA, USA); detailed genotyping and quality control information for this sample can be found in Edenberg et al.20 The European-American and African-American participants in the case–control sample were imputed together (n=1884). Prior to imputation, monomorphic SNPs (that is, SNPs with a minor allele frequency <0.0001), SNPs with missingness >2%, SNPs with Hardy–Weinberg equilibrium P<1 × 10−6 and SNPs that did not map to the Hg19 reference genome were filtered out, leaving 936 240 SNPs. Phasing of entire chromosomes or chromosome arms was performed using SHAPEIT.23, 24 Genotype imputation of additional SNPs was carried out with IMPUTE2 v.2.031 using the March 2012 release (v3) of the 1000 Genomes Project data (www.1000genomes.org25). Imputation analysis was performed for genomic windows of 5 Mb with an overlap interval of 500 kb between adjacent segments. Following the recommendations of the authors of IMPUTE2, we did not limit our imputation procedure to European reference samples. Monomorphic sites were excluded.
