Quality control checks were applied to ensure quality of both the phenotypes and genotypes. For each phenotype and covariate, distribution statistics including the minimum, maximum, quartiles, median, mean, and standard deviation were examined. We ensured that these statistics were within expected limits given the phenotype definitions and any scale transformations per the analysis plan. We also evaluated simple relationships among phenotypes. When discrepancies were noted we contacted the original study for clarification or re-analysis, or the data were removed from further analysis. Phenotypic statistics are presented in Supplementary Tables 6 and 7.
