We applied our method to 21,497 African-American individuals from the WHI, CARe, and AAPC cohorts over a total of 12 quantitative phenotypes and 1 case-control phenotype (see Online Methods). Local ancestry was inferred using the HAPMIX, SABER+, and RFMix methods, which are extremely accurate in African Americans (r2=0.98 or greater)22,23,24. For each phenotype we estimated hg2, hγ2 and by extension h2. For hg2 and hγ2 we used the GCTA software package applied to the genotypes and local ancestry at each SNP respectively17. For those phenotypes measured in both cohorts we compute the inverse variance-weighted mean and standard error. For each phenotype we also list previously published estimates of heritability from family studies using twins and African-American estimates where available ( hpub2) The results are shown in Table 3, and published African-American estimates are marked for reference. Estimates from European populations may not be directly comparable if the genetic or environmental bases for the phenotype differ substantially.
