We found that regional heterogeneity in the action of cis-eQTL signals was evident not only from variable signal strength, but also from variability in their target of action. Excluding average-all signals, our data set contained 44,270 cis-eQTL subsignals (sentinel–expression ID–region combinations) involving 12,748 sentinels. 9,384 of these sentinels (73.6%) regulated a single gene in a single brain region only, while 2,762 (21.6%) regulated a single gene across multiple brain regions. Intriguingly, 602 of these sentinels cis-regulated multiple genes, with a maximum of 10 genes regulated by the same marker (Supplementary Table 6). 312 of these regulated different genes with at least one marker–gene relationship being unique to a single brain region, and 96 of these sentinels regulated multiple gene targets all of which were region specific (as based on the absence of a significant cis-eQTL signal in another brain region and on significant regional heterogeneity using our modified test of heterogeneity). One of the most interesting examples of such markers is rs73009150, which was a cis-eQTL signal for RNF214 in medulla, for PAFAH1B2 in cerebellum and putamen, and for SIK3
