(and population) and analyzed in depth those associations significant at the 0.001 permutation threshold (see Supplementary Methods). At this level of significance, we expect approximately 14 genes to have at least one significant association by chance, and we detect 299, 318, 341 and 394 for CEU, CHB, JPT and YRI, respectively, with a false discovery rate (FDR) of 4-5% per population (Table 1 and Table S1). In total, there is a non-redundant set of 831 genes exhibiting a significant cis- association in at least one population, 310 genes in at least two populations, and 62 in all four. As expected, due to the small sample size, the detected genetic effects are large, with R2 values ranging from 0.27 to close to 1. A total of 209 out of 299 CEU-significant genes and 247 out of 394 YRI-significant genes had heritability estimates above 0.2. Of the set of 831 genes with significant cis associations, 431 had heritability estimates above 0.2. Heritability overall correlated reasonably well with cis-association significance (Figure S4) but the heritability estimates have large variance and are to be taken with caution on a per gene basis. When evaluated in the context of GO-slim terms, we detected a significant
