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Table 5 Putative UTR regulatory elements affected by cancer-associated UTR-SNPs.

From: In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions

  UTR-SNPs Ref (n = 20,304) UTR-SNPs Var (n = 20,304) CANCER Ref (n = 358) CANCER Var (n = 358) CANCER Ref (permutation pool, n = 92) CANCER Var (permutation pool, n = 92)
Total IRES 5766 5802 92 94 20 20
Gained   625   11   3
Lost   589   9   3
Total 15-LOX-DICE 1788 1744 37 36 8 8
Gained   90   2   
Lost   134   3   
Total TOP 491 490 11 10 5 5
Gained   1     
Lost   2   1   
Total K-Box 287 287 3 3 0 0
Gained   16     
Lost   16     
Total GY-Box 174 168 5 5 0 0
Gained   9     
Lost   15     
Total Brd-Box 111 116 2 1 1 0
Gained   13     
Lost   8   1   1
Total ADH-DRE 44 50 1 1 1 1
Gained   6     
Lost   0     
Total CPE 26 30 1 1 0 0
Gained   12     
Lost   1     
Total SECIS-2 12 10 1 0 1 0
Gained   1     
Lost   3   1   1
  1. The results identify cis-regulatory elements located in the immediate vicinity of or at the UTR-SNP sites. UTR regulatory elements can be 'gained' or 'lost' when reference allele sequences are modified by cancer-associated SNPs.