We also found cis-eQTL signals that were only detected in a specific brain region, varying from 936 in substantia nigra to 4,642 in cerebellum (Fig. 2b). We note that some of these single-region cis-eQTL signals will result from the chance detection of a weak pan-regional signal in one region only. We therefore investigated the statistical evidence for regional heterogeneity using a modified test of heterogeneity (see Online Methods). This test was specifically used to distinguish between the absence of a cis-eQTL signal in a brain region and the failure of a cis-eQTL signal to reach statistical significance in the presence of expression. We found 42.6% of the 17,374 tested cis-eQTL subsignals to be heterogeneous (Supplementary Table 5). The regional heterogeneity of these eQTL signals could not be explained by absence of gene expression in some regions, as regions with no detectable expression above background were excluded from the test-of-heterogeneity analysis.
