Cell-type specific marks, including genome-wide long-range interactions, active promoter/enhancer/insulator marks, predicted ChromHMM maps, as well as a user-defined promoter region, are then used to identify the potential regulatory effects of the variants. We defined a variant mapped onto any of these regions as a ‘GWAS3D signal’, which implies a relevant regulatory function such as affecting distal interaction in high dimension or direct promoter activity of a target gene. The variants that are not mapped to any regulatory regions are filtered out at this stage.
