Intervene Shiny App provides an interactive interface for intersection and effective visualization of gene or genomic region sets. Currently, Shiny app does not acccept genomic regions as input, but the text files generated by Interve's command line interface can be easily uploaded to further explore and customize the plots in an interactive way.
Intervene has three modules: venn to generate Venn diagrams of up-to 6 sets, upset to generate UpSet plots of more than 3 sets and pairwise to compute and visualize pariwise intersections as clustered heatmap.