I shared a history (using chr22 data for simplicity):
and a workflow:
with you that do the trick. Basically, you
1. download mRNA data as BED and as mRNA sequences (history items 1 &
2. Collapse sequences to tab-delimited format (history item 3)
3. Remove dots and numbers by replacing dots with tabs and cutting
accession and sequence out (History items 4 & 5)
4. Join sequences with bed file (History item 6)
5. Downloading the SNPs (History item # 7)
6. Joining with SNPs (History item # 8).
You can use workflow to run this analysis genomewide.
Let me know if you have issues.