The GWAS catalogue provides a rich functional categorization from the precise phenotypes being studied. These phenotypic categorizations are non-randomly associated with ENCODE annotations and there is striking correspondence between the phenotype and the identity of the cell type or TF used in the ENCODE assay (Figure 10B). For example, five SNPs associated with Crohn’s disease overlap GATA2-binding sites (P-value 0.003 by random permutation or 0.001 by an empirical approach comparing to the GWAS-matched SNPs; see Supplementary information), and fourteen are located in DHSs found in immunologically relevant cell types. A notable example is a gene desert on chromosome 5p13.1 containing eight SNPs associated with inflammatory diseases. Several are close to or within DHSs in Th1 and Th2 cells as well as peaks of binding by TFs in HUVECs (Figure 10C). The latter cell line is not immunological, but factor occupancy detected there could be a proxy for binding of a more relevant factor, such as GATA3, in T-cells. Genetic variants in this region also affect expression levels of PTGER477, encoding the prostaglandin receptor EP4. Thus, the ENCODE data reinforce the
