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

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

	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

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.

ISSN: 1471-2164