Each cohort was imputed using SHAPEIT51 and IMPUTE252, using the cosmopolitan (all ancestries) 1000 Genomes reference panel consistent with prior recommendations53 (see also47,54,55). Concordance of minor allele frequencies (MAF) with the reference panel was verified prior to imputation, with SNPs in EU cohorts compared to MAF in European population samples and AA cohorts compared to MAF in African population samples (Supplementary Information A4). Cryptic relatedness between cohorts was excluded after imputation (Supplementary Information A5). Imputed SNPs were then filtered for INFO score > 0.8 and allele frequency > 0.01 prior to analysis.
