SNP45. We therefore can approximately estimate neff of GTEx-brain assuming constant mean q2 across brain regions (Supplementary Note 2). Note that this assumption is justified by the highly consistent estimates of variance of cis-eQTL effects across genes in different brain regions (Supplementary Fig. 21) along with a mean rb estimate of 0.94 between pairwise brain regions for cis-eQTL effects in SD units. The estimate of neff of GTEx-brain was 233, approximately 2.6 times larger than the actual sample size of brain tissue in GTEx (mean n = ~89 across 10 brain regions) (Supplementary Fig. 20d). To further increase the power of detecting brain eQTLs, we meta-analyzed GTEx-brain, CMC, and ROSMAP (referred to as Brain-eMeta hereafter). The gain of power is demonstrated by the increased number of genes with at least one cis-eQTL with PeQTL < 5 × 10−8 in Brain-eMeta as compared with that in GTEx-brain, CMC, or ROSMAP (Fig. 5a).
