Part 4:  Finding SNPs that are likely to be phenotype associated.

1. Bring in a gene set
2. Finding coding SNPs that cause a change in amino acid
3. Compute flanking regions of exons
4. Finding SNPs that may cause a change in splicing
5. Bring in ENCODE segmentations
6. Filter for promoters and enhancers
7. Find SNPs in promoters and enhancers