gene region. Chromatin interaction mapping can involve long-range interactions as it does not have a distance boundary. FUMA currently contains Hi-C data of 14 tissue types from the study of Schmitt et al51. Since chromatin interactions are often defined in a certain resolution, such as 40kb, an interacting region can span multiple genes. If a SNPs is located in a region that interacts with a region containing multiple genes, it will be mapped to each of those genes. To further prioritize candidate genes, we selected only interaction-mapped genes in which one region involved in the interaction overlaps with a predicted enhancer region in any of the 111 tissue/cell types from the Roadmap Epigenomics Project46 and the other region is located in a gene promoter region (250bp up and 500bp downstream of the transcription start site and also predicted by Roadmap to be a promoter region). This reduces the number of genes mapped but increases the likelihood that those identified will have a plausible biological function. We used a FDR of 1×10−5 to define significant interactions, based on previous recommendations51 modified to account for the differences in cell lines used here.
