If you go back to the PhenCode Basic Browser Tracks page and make different selections, each new custom track will replace the previous version. However, unselecting a data source will not delete the corresponding track; use the Browser's "manage custom tracks" button to do this.
Another track that can be useful to view alongside the variants is the ORegAnno track, which contains literature-curated regulatory elements. This is a resident track rather than a custom one; it is not displayed by default, but is located in the "Expression and Regulation" section and can be opened by choosing "pack" in the track controls below the image. (If you have set the Browser not to show the controls below the image, you can access them by clicking the "configure" button.)
The track is a resident track at the BX Genome Browser (partial mirror of the UCSC Genome Browser at Penn State). You will find the track under Variation and Repeats and labeled "Locus Variants". Set the track to pack and click refresh.
Go to the Ensembl Human browser and select Manage your data. Then select Attach DAS. PhenCode is included in the DAS Registry so just click Next, find PhenCode in the list that is produced and select it. The PhenCode track will be available then.