To increase the power of our analysis we ran the cis- association analysis using the REDUCED data (see Methods) and the same analysis parameters, and at the 0.01 permutation threshold detected 1,966, 1,950, 1,984, 2,131, 1,794, 1,131, 2,562, 2,415, genes with a significant association in CEU, CHB, GIH, JPT, LWK, MEX, MKK, and YRI, respectively with a false discovery rate (FDR) of 7–16% per population (Table 2). In total, there is a non-redundant set of 5,691 genes showing a significant cis association in at least one population, 3,240 in at least two populations, and 331 in all eight populations. This indicates that 57% of genes with a significant cis-association had an association in at least two of the populations, which is an increase over the 34% replication observed using the normalized and PCA-corrrected data (Table 1). As expected given each population's sample size, all significant detected effects are relatively large; the range of Spearman's rho, the correlation coefficient, is 0.338–0.919 for the normalized and PCA-corrected data, and 0.337–0.933 for the ‘REDUCED data’ (Table S4). There is substantial overlap between genes
