GCTA27, 28, 29 was used to estimate SNP-chip heritability (h2SNP) in the EA and AA subsamples (separately) as follows: following QC, data sets were combined using PLINK18, 30 (that is, the 7 EA bed/bim/fam file sets were combined into one EA7 bed/bim/fam file set). Genetic relationship matrices (GRMs) were made (one chromosome at a time for computational efficiency) using ‘—chr n’ for chromosomes 1–22, ‘—maf 0.01’ to restrict to SNPs with MAF >1%, ‘—make-grm-bin’ to make the GRMs and then combined with ‘—mgrm’ command. Heritability estimation with ‘—reml-no-constrain’ command, specifying a GRM with ‘—grm-bin’, a phenotype file with ‘—pheno’, prevalence with ‘—prevalence’ quantitative covariates (here, PCs 1–10) with ‘—qcovar' and binary covariates (here, sex and study indicator covariates) with ‘—covar’. Prevalence was specified as 11% (females), 5% (males) and 8% (combined).
