For each variant detected by GWAS3D, we provided six annotations, including variant summary, binding affinity, GWAS3D signals, genomic elements, LD signals and external annotation. Users can systematically analyze the regulatory properties of variants based on these annotations. First tab is about variant summary, showing the important attributes related to the selected variant and reports the information of previous GWAS result recorded in GWASdb (39) for this variant. In the tab of binding affinity, we listed top five significant affinity differences of TF motifs with detailed binding sites information. For the GWAS3D signals information, we offered a tab to show all of mapped functional elements used in GWAS3D and related marks information. To help user identify all putative regulatory variants in the LD of observed leading variant, we used one additional tab to list related information. Lastly, three useful external browsers were encapsulated into the system to give broad annotations and predictions including GWASrap (40), RegulomeDB and UCSC ENCODE genome browser. User can directly fetch the information in an internal window.
