How to predict the effect of a non coding SNP variant on the expressed protein?
A) Generate exon &amp; transcript counts for your samples, library size + quantile normalize the data.
B) Group samples into variant/wild-type categories
C) Use wilcoxon's rank sum test to see if there are differences in exon inclusion or overall expression. Remember that 3'UTR variants can also imply differential degradation by miRNA. Tools like TargetScan can help you with miR-analysis.