Leveraging molecular QTL to understand the genetic architecture of diseases and complex traits

There is increasing evidence that many GWAS risk loci are molecular QTL for gene expression (eQTL), histone modification (hQTL), splicing (sQTL), and/or DNA methylation (meQTL). Here, we introduce a new set of functional annotations based on causal posterior probabilities (CPP) of fine-mapped molecular cis-QTL, using data from the GTEx and BLUEPRINT consortia. We show that these annotations are very strongly enriched for disease heritability across 41 independent diseases and complex traits (average $N$=320K): 5.84x for GTEx eQTL, and 5.44x for eQTL, 4.27-4.28x for hQTL (H3K27ac and H3K4me1), 3.61x for sQTL and 2.81x for meQTL in BLUEPRINT (all P < 1.39e-10), far higher than enrichments obtained using standard functional annotations that include all significant molecular cis-QTL (1.17-1.80x). eQTL annotations that were obtained by meta-analyzing all 44 GTEx tissues generally performed best, but tissue-specific blood eQTL annotations produced stronger enrichments for autoimmune diseases and blood cell traits and tissue-specific brain eQTL annotations produced stronger enrichments for brain-related diseases and traits, despite high cis-genetic correlations of eQTL effect sizes across tissues. Notably, eQTL annotations restricted to loss-of-function intolerant genes from ExAC were even more strongly enriched for disease heritability (17.09x; vs. 5.84x for all genes; P = 4.90e-17 for difference). All molecular QTL except sQTL remained significantly enriched for disease heritability in a joint analysis conditioned on each other and on a broad set of functional annotations from previous studies, implying that each of these annotations is uniquely informative for disease and complex trait architectures.