Toolbox | Track Tools () | Annotate and Filter | Annotate with Overlap Information
First, select the track you wish to annotate and click Next. You can choose any kind of annotation track as input. Next, select the variant track for overlap comparison.
The result of this tool is a new track with all the annotations from the input track and with additional information from the annotations that overlap from the other track. The requirement for being registered as an overlap is that parts of the annotations are overlapping, regardless of the strandedness of the annotations (note that this makes it unsuitable for comparing e.g. two gene tracks but great for annotating variants with overlapping genes or regulatory regions).
When running the "Annotate with overlap information" tool with a gene track as input and a variant track as parameter track, a new column describing the specific variant is added to the Track Table. The variant description also appears in the track tooltips when mousing over the individual variants.