We illustrate the value of our eQTL data set for some important brain-related GWAS signals. rs2395163 is a risk SNP for Parkinson’s disease32, but is challenging to interpret given that it is an intergenic SNP located in the major histocompatibility complex region of chromosome 6, a highly gene-rich region with high levels of linkage disequilibrium. In our data this SNP is a significant gene-level and exon-level cis-eQTL for HLA-DQA2 (P = 1.29 × 10−6 in the inferior olivary nucleus of the medulla and P = 1.82 × 10−12 in average-all for expression ID 2903265; Fig. 7a) and a more moderate exon-level cis-eQTL for BAT3 (P = 3.64 × 10−6 in average-all for expression ID 2949194). Both HLA-DQA2 and BAT3 are located on the other side of a recombination hotspot, and we note that the cis-eQTL signal for HLA-DQA2 is significantly stronger.
