I am planning on doing something similar! However I am not doing epigenetics, but rather a slightly different route. I was debating between going with Integrative Biology at CLAS (with Bioinformatics/Chemistry minors) or Biotechnology at CALS (with Bioinformatics/Wildlife Conservation minors).
I made a chart of the courses I would be taking for either and I added Biochemistry in as well. It is run on the assumption that all pre-reqs and orgo have been completed, but I think it could be of use to you if you factor in your minors and get rid of my Wildlife Conservation minor (WIS courses and an ecology course). It also doesn’t include the two electives for Biotechnology, since there was no specification on which courses they were. My assumption is they are the immunology/virology courses.
https://drive.google.com/file/d/0B96zMzz0RZ2EdnNJYTZsdXlWXzQ/view?usp=sharing
As for your question, I don’t believe there is a stigma for graduate schools against biology. Most schools I have been looking into state they would like a biology major, or something closely related. I feel (and hope) they are going to look at the courses you have taken and their application towards what you are going to be doing.