Finally, using chromatin interaction, SNPs were mapped to genes based on a significant chromatin interaction between a genomic region in a risk locus and promoter regions of genes (250 bp up- and 500 bp downstream of transcription start site (TSS)). Unlike eQTL mapping, chromatin interaction mapping has no distance boundary and can involve long-range interactions. Currently, Hi-C data of 14 tissue types are included in FUMA46. Generally, chromatin interactions are defined in a certain resolution (40 kb in this case) such that interacting regions may span multiple genes. All SNPs within these regions would be mapped by this method to genes in the corresponding interaction region. To further prioritize candidate genes from chromatin interaction mapping, we integrated predicted enhancers and promoters in 111 tissue/cell types from the Roadmap Epigenomics Project45; chromatin interactions are selected in which one region involved in the interaction overlaps with predicted enhancers and the other region overlaps with predicted promoters in 250 bp upstream and 500 bp downstream of the TSS site of a gene. A FDR of 1 × 10−5 was applied to define significant interactions.
