12). Despite the limited sample size, we identified 477 cis-eQTL genes that are significant in Cerebellum-EUR but not in Cortex-EUR (Supplementary Fig. 13), perhaps due to low expression in the cortex or because they are regulated by transcription factors that are more active in the cerebellum (Supplementary Note and Supplementary Table 6). Next, we repeated Cortex-EUR eQTL discovery while excluding GTEx and compared the results with cis-eQTLs from different GTEx tissues (Fig. 3e, Supplementary Figs. 12,14 and Supplementary Table 5). There was high agreement between brain-related tissues (cerebral tissues, Rb > 0.8, caFC > 0.71 and AC > 96%; and cerebellar tissues, Rb > 0.76, caFC > 0.71, π1 > 0.55 and AC > 92%) compared with other tissue types. The lowest agreement was with tissues such as testis (Rb = 0.51, caFC = 0.48 and AC = 78%) and whole blood (Rb = 0.55, caFC = 0.53 and AC = 80%). The π1 scores were not higher for cerebral or cerebellar tissues compared with non-brain tissues. We also compared Cortex-EUR cis-eQTLs with eQTLGen14 (n = 31,684; blood-based, majority EUR ancestry), which supported the low agreement observed in GTEx blood. Of the overlapping eQTLs, 25% had an opposite allelic effect
