Toolbox | Add Information to Variants () | Add Information from genomic regions ()
First, select the track you wish to annotate and click Next. You can choose any kind of variant or annotation track as input. Next, select the track holding the overlapping region of interest (e.g. regulatory regions from ENCODE or if you have imported other databases containing regions that you would like to use for overlap comparison).
The result of this tool is a new track showing all the variants that now have been annotated with the information about the regions that overlap with the identified variants. The requirement for being registered as an overlap is that parts of the annotations are overlapping, regardless of the strandedness of the annotations. The added information can be visualized in two ways; 1) In the track tooltips when mousing over the individual variants or 2) in the table view where you can see that new columns describing the added overlap information have been added to the table. The table view can be accessed by clicking on the table icon () in the lower part of the View Area.