Many of them reside in important cancer-related genes, such as ATRX, BCOR, CDKN2B, MAP3K1, MAP3K4, MDM2, SMAD4, STK11, and TP53. We also discover alternative splicing phenomena enriched in non-coding regions, such as new exon creation being the dominant splice alteration event. This evidence concerns the gene SMAD4 and cancer.