You are underestimating the cost of living in SD. All three programs are quality programs. If you were going for Neuroscience, it would push for SD, but it seems that your interest is on Genomics/Epigenetics. Scripps is strong in those fields, but other institutions are stronger. Again, congratulations on your acceptances. You are not going to make a "wrong" choice, go with the program that excited you the most in terms of their science. These are great decisions to make!