Genotyping in all cohorts was carried out on Illumina or Affymetrix platforms, after which quality control (QC) was performed, followed by imputation of genotypes. QC of genotype data was performed in each cohort separately, with comparable but cohort specific criteria. Standard QC checks included tests of European ancestry, sex inconsistencies, Mendelian errors, and high genome-wide homozygosity. Checks for relatedness were conducted in those cohorts that aimed to include unrelated individuals only. Other checks of genotype data were based on minor allele frequencies (MAF), SNP call rate (% of subjects with missing genotypes per SNP), sample call rate (% of missing SNPs per subject) and Hardy–Weinberg Equilibrium (HWE). Genotype data were imputed using the 1000Genomes phase 1 version 3 (build37, hg19) reference panel with standard software packages such as IMPUTE, MACH, or Minimac, see Supplementary Table 1.
