Two semi-independent analysts (JJT and EU) performed stringent within-cohort quality control, filtering out poor performing SNPs. SNPs were excluded if they met any of the following criteria: study-specific minor allele frequency (MAF) corresponding to a minor allele count < 100, poor imputation quality ((INFO/R2) score <0.6), and/or Hardy–Weinberg equilibrium p < 5 × 10−6. Moreover, we excluded SNPs and indels that were ambiguous (A/T or C/G with MAF > 0.4), duplicated, monomorphic, multiallelic, or reference-mismatched (Supplementary Note 2 and Supplementary Table 17). Then, we visually inspected the distribution of the summary statistics by creating quantile–quantile plots and Manhattan plots for the cleaned summary statistics from each cohort (Supplementary Notes 4-6). Discrepancies between the results files of the two semi-independent analysts were examined and errors corrected.
