YRI, respectively with a false discovery rate (FDR) of 18–39% per population (Table 1). Similar FDR values were obtained when evaluating the degree of replication of an eQTL discovered in one population by replication in another (see Methods) where FDR was estimated to range from 31% to 40%. A lower FDR was observed in non-African populations as expected, given that only a subset of African eQTLs will be represented in non-African samples. In total, at the 0.01 threshold we detected a non-redundant set of 3,130 genes exhibiting a significant cis association in at least one population. At higher stringency (permutation threshold 0.001), the per-population FDR ranged from 4%–11%; with a total of 1,132 genes exhibiting a significant cis association in at least one population.
