We have designed a web-based tool to detect, prioritize and annotate the regulatory genetic variations in combination with experimental data and computational predictions. Particularly, this tool takes advantage of recently generated ENCODE data, especially the experimental long-range interactions as well as the active marks of functional elements, to predict variants in the putative TFBSs in distal and proximal promoter regions. GWAS3D is a tool dedicated to detect true functional variants that control gene regulation for genetic studies. Compared with recent software and databases such as VAAST, HaploReg and RegulomeDB, GWAS3D integrates more features and can be used in many scenarios. User can identify the most probable functional variant associated with interesting trait in one risk locus or prioritize the leading variants when given a full list of GWAS result or evaluate the deleteriousness of genetic variants affecting the gene regulation without any prior effect. GWAS3D also provides flexible configurations, such as human population, cell type specificity and TF family classification, for users to deal with different aspects of complex disease/trait. For example, user may select a matched cell type/tissue satisfying
