As we announced in our e80 release post, we rolled out a prototype display for cis-regulatory interactions, essentially arches connecting any two elements on the same chromosome. This was mainly designed to display your eQTL or Hi-C with little effort, based on the WashU Epigenomics Explorer interaction track:
All you need to do is prepare a tab-delimited interaction file, optionally indexing it with Tabix if it is too large to upload directly. You can use it to represent Intra-chromosomal rearrangements such as the micro-inversion below:
@RNA3DHub even suggested using it to display RNA secondary structure:
You can do what you want really!