Using one of the largest multi-omic datasets for brain tissue, we generated a list of xQTLs as a Resource for the neuroscience community to further investigate the interplay between the genome, epigenome, and transcriptome in disease susceptibility. Our list of xQTLs replicates well in both brain and blood datasets, but it also contains xQTLs that appear unique to brain. Notable biological insights drawn from this Resource include significant sharing of xQTL SNPs across the measured molecular phenotypes. Also, the effects of some eQTL SNPs are fully mediated by our two epigenetic features, but further work and more data are needed to comprehensively assess the extent to which epigenomic features mediate eQTL effects. Overall, we created a large new reference with which investigators can functionally annotate their results, enhance their analyses as illustrated by our xQTL-weighted GWAS approach, and guide functional studies as with our cell type analysis. This Resource can be easily accessed through our portal, xQTL Serve.
