All imputed autosomal variants with IMPUTE information score > 0.4 (M = 39,723,562) were eligible for association testing in phenotype-specific models. An effective sample size (Neff) was calculated for each SNP in a given phenotype-specific model, where Neff = 2 × MAF × (1 — MAF) × N × info where MAF is the minor allele frequency among the set of individuals included in a phenotype-specific model, N is the total sample size for a given phenotype and info is the IMPUTE information score of the SNP. Variants with Neff < 30 (continuous phenotypes) or Neff < 50 (binary phenotypes), were excluded from the final set of phenotype-specific results. The number of variants analysed per trait ranged from 21,894,105 to 34,656,550 for continuous phenotypes and 11,665,604 to 28,263,875 for binary phenotypes (Supplementary Table 1). Quantile–quantile plots and λGC (GC = genomic control) were used to assess genomic inflation in all phenotypes, for which λGC ranged from 0.98 to 1.15. Single-variant association testing for each phenotype used an additive model that was adjusted by indicators for study, self-identified race/ethnicity, the first
