For each pairwise combination of populations, we examined those SNP-probe pairs that were significant in both populations and determined the proportion that had the allelic effect in the same direction in both populations. As described above, at the 0.01 permutation threshold we detected 1,074 genes with a significant cis- association in at least two populations. Among the 28 population pairs, we observed 98.9–100% concordance of allelic direction (Figure 1). Evaluation of allelic direction concordance from the ‘REDUCED data’ analysis produced nearly identical results (not shown). These results suggest that regulatory variation affects gene expression in the same direction across populations.
