As cis-eQTLs associated with probes overlaying SNPs need to be interpreted with caution, we examined our significant associations for potential artifacts. At the 0.01 permutation threshold, of the 3,292 probes with significant associations (corresponding to 3,130 genes), 249 probes (245 genes), overlaid a SNP. This means that 7.5% of the probes with a significant cis-eQTL overlaid a common SNP (compared to 6.5% among all probes), which did not represent a significant enrichment of these probes among our significant associations. We did, however, consider the effect of these associations on across-population sharing of associations, and report levels of sharing both with and without these probes. At the 0.01 permutation threshold, of the 3,130 genes exhibiting a significant cis association, 1,074 genes had a significant association in at least two populations, and 63 in all eight populations. This indicates that 34% of genes with a significant cis-association had an association in at least two of the populations, and 2% of genes in all eight populations. If we conservatively exclude those probes known to overlap common SNPs, we reduce the number of non-redundant
