In addition to GWAS, functional genomics data provides evidence for the effect of variants on genes (Figure 1A). Molecular phenotype quantitative trait loci data (QTLs) includes protein QTL (pQTL) data of 2994 plasma proteins assessed in 3301 individuals of European descent (9). Gene expression QTLs (eQTLs) are integrated from the eQTL Catalogue, eQTLGen and GTEx (https://www.gtexportal.org/home/) (10,11). Other datasets that provide evidence for variant to gene (V2G) association include epigenetics chromatin conformation and interaction experiments with promoter capture hiC (PCHI-C) from 27 different cell types, enhancer-TSS pairwise cap analysis of gene expression (CAGE) correlation, and DNase I hypersensitive site (DHS)-gene promoter correlation (12–14). Each epigenetic data point is represented as a pair of interacting genomic intervals and an association statistic. Interval pairs are retained with one end encompassing an Ensembl gene Transcription Start Site (TSS) and the other end containing any variant in GnomAD 2.1 (Figure 1B) (15,16).
