All GWAS were conducted among individuals that (a) were of European ancestry, (b) were not missing any relevant covariates, (c) were successfully genotyped and passed standardized sample-level quality control (according to study-specific protocols13–16,18), and (d) were unrelated (unless a particular GWAS was conducted with linear mixed models). Genotypes were imputed with reference data from either the 1000 Genomes Consortium62, the Haplotype Reference Consortium63, the UK10K Consortium64, or a combination thereof. We performed quality control with EasyQC (version 9.1)65. For that purpose, we used a whole-genome sequenced reference panel, assembled from 1000 Genomes Consortium62 and UK10K Consortium64 data by using BCFtools (version 1.8; Supplementary Information section 2.4.1). Our quality-control procedure applied recommended65 SNP-filtering to (i) remove rare SNPs (minor allele frequency < 0.005), (ii) SNPs with an IMPUTE imputation quality (INFO) score less than 0.9, (iii) SNPs that could not be mapped to or had discrepant alleles with the reference panel, and (iv) otherwise low-quality variants (Supplementary Table 2). For a complete description of the quality-control, see Supplementary Information section 2.4.
