We did not find any examples of cis-eQTL subsignals that significantly reversed slopes in different brain regions, a phenomenon that has been reported in pure cell types26, perhaps because our brain samples comprised mixtures of cell types. Statistically significant heterogeneity generally manifested itself as a significant slope in some regions and a lack of a slope in others. In some cases, as demonstrated by the example of rs10788102, a significantly heterogeneous cis-eQTL for PPADC1A (Fig. 3b), the eQTL signal was only evident in a single brain region (cerebellum). Conversely, significant regional heterogeneity in cis-eQTL signals could also arise by the detection of cis-eQTL signals in all but one brain region. One such example is rs48888622, a significantly heterogeneous cis-eQTL for ADAMTS18 (Fig. 3c). Although ADAMTS18 was most highly expressed in cerebellum, this was the only brain region where a cis-eQTL signal was not evident. This last example also illustrates that eQTL detection is not purely driven by differences in overall gene expression.
