Expression quantitative trait locus (eQTL) analyses4–6 have been very useful in understanding the functional consequences of trait- and disease-associated variants and in identifying genes that are likely to be affected by a risk allele. Recently, QTL analyses have been extended to other molecular phenotypes, such as DNA methylation (mQTL)7,8 and histone modification (haQTL)9. Overall, SNPs associated with molecular phenotypes (xQTLs) are over-represented among SNPs that are linked to various traits and diseases6,10, and previous studies have used eQTL hits to prioritize associations in GWAS, leading to improved detection sensitivity11–13. While a few datasets exist for brain tissue, large datasets measuring all three of these epigenomic and transcriptomic features have only recently been generated from the same brain region of the same individuals.
