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Table 2 Summary of cancer-associated UTR-SNPs.

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

Description

SNP ID

UTR

Variation

P value

mRNA secondary structure distance

Putative functional element

SPARC precursor [P09486/ENST00000231061]

rs1059829

3'

c

2072

t

4,67E-17

38

 

Histidine triad nucleotide-binding protein 1 [P49773/ENST00000304043]

 

3'

t

483

g

5,00E-17

62

IRES

Ig alpha-1 chain C region [P01876/ENST00000251006]

 

3'

g

1643

a

8,27E-17

78

IRES

Annexin A1 [P04083/ENST00000257497]

rs3739956

5'

a

58

g

1,47E-12

8

 

Lithostathine 1 alpha precursor [P05451/ENST00000233735]

 

3'

c

718

t

1,17E-11

0

 

26S proteasome-associated pad1 homolog [NM_005805/ENST00000263639]

rs9713

5'

a

460

t

3,87E-10

12

 

Glucagon precursor [P01275/ENST00000233604]

 

3'

g

698

a

8,16E-09

6

IRES *

mitochondrial ribosomal protein L41 [NM_032477/ENST00000332183]

rs698148

3'

g

526

c

1,92E-08

6

IRES

Actin, cytoplasmic 2 (Gamma-actin) [P02571/ENST00000331925]

 

3'

g

1572

a

5,92E-08

0

IRES

Biglycan precursor [P21810/ENST00000331595]

 

5'

g

94

t

6,45E-08

4

15-LOX-DICE

Mitochondrial processing peptidase alpha subunit [Q10713/ENST00000298536]

rs7628

3'

a

1933

g

8,04E-08

68

ADH_DRE

Beta-2-glycoprotein I precursor [P02749/ENST00000205948]

rs6933

3'

c

1090

t

5,35E-07

0

 

SH3-containing GRB2-like protein 1 [Q99961/ENST00000269886]

 

3'

c

2116

t

1,18E-06

38

 

dynactin p62 subunit [NM_016221/ENST00000255263]

 

3'

c

3575

t

5,57E-06

26

IRES

Interleukin-4 receptor alpha chain precursor [P24394/ENST00000170630]

rs8832

3'

a

3135

g

1,12E-05

52

 

Ran GTPase [P17080/ENST00000254675]

 

3'

g

900

a

1,32E-05

0

IRES *

Chemokine-like factor super family member 6 [Q9NX76/ENST00000205636]

 

3'

t

3549

a

1,44E-05

14

 

60S ribosomal protein L29 [P47914/ENST00000294189]

 

3'

c

613

a

1,92E-05

4

 

14-3-3 protein zeta/delta [P29312/ENST00000297569]

rs11551356

3'

t

2351

c

2,02E-05

0

 

TC4 protein [Q96QB7/ENST00000316561]

 

3'

g

841

a

5,15E-05

48

 

Metallothionein-IE [P04732/ENST00000306061]

rs708274

3'

g

209

t

5,30E-05

66

 

Retinoic acid- inducible E3 protein [Q13571/ENST00000294507]

rs1050739

3'

g

2125

a

7,38E-05

12

IRES *

Voltage-dependent anion-selective channel protein 2 [P45880/ENST00000298468]

rs11543

5'

g

51

c

9,91E-05

64

 

PDZ and LIM domain protein 1 [O00151/ENST00000265995]

rs1049989

3'

t

1193

g

1,17E-04

0

 

Pituitary tumor-transforming protein binding factor [P53801/ENST00000330938]

 

3'

c

2723

t

1,33E-04

8

 

Mitochondrial import receptor TOM22 homolog [Q9NS69/ENST00000216034]

rs1056691

3'

t

966

g

1,44E-04

48

 

Ubiquitin-like protein SUMO-1 conjugating enzyme [P50550/ENST00000219558]

rs7302

3'

t

1024

g

1,55E-04

16

IRES

Dynein light chain 1 [Q15701/ENST00000242577]

 

5'

t

45

c

1,73E-04

22

 

20 kDa nuclear cap binding protein [P52298/ENST00000321256]

 

3'

a

1683

c

1,80E-04

0

 

Cytochrome P450 1B1 [Q16678/ENST00000260630]

rs162549

3'

a

4412

t

1,84E-04

6

 

PTD012 protein [NM_014039/ENST00000332038]

 

3'

a

2118

g

1,98E-04

74

 

Small proline-rich protein 3 [Q9UBC9/ENST00000295367]

rs1134220

3'

t

958

g

2,14E-04

68

 

Large neutral amino acids transporter small subunit 2 [Q9UHI5/ENST00000316902]

 

3'

c

2689

t

2,25E-04

0

 

Transforming protein p21A Ki-Ras [P01116/ENST00000311936]

 

3'

t

1260

c

2,51E-04

10

IRES

nucleolar protein family A, member 3 [NM_018648/ENST00000328848]

rs1045238

3'

g

327

c

3,07E-04

58

TOP

Heterogeneous nuclear ribonucleoprotein K [Q07244/ENST00000297818]

rs167203

5'

c

156

g

3,50E-04

10

 

RECS1 protein homolog [Q969X1/ENST00000258412]

 

3'

g

2920

a

3,70E-04

0

 

G1/S-specific cyclin D2 [P30279/ENST00000261254]

 

3'

a

6471

c

3,78E-04

20

 

Zinc finger protein 384 [Q8TF68/ENST00000319770]

rs6786

3'

t

3145

c

4,32E-04

0

 

Myosin regulatory light chain 2 [P19105/ENST00000217652]

rs7811

3'

a

1107

g

4,68E-04

22

 

Neuron specific protein family member 2 [Q9Y328/ENST00000303177]

rs4457100

3'

a

1030

g

5,46E-04

8

 

Sorting nexin 4 [O95219/ENST00000251775]

 

3'

t

2178

a

5,63E-04

ND

IRES *

Paired amphipathic helix protein Sin3b [O75182/ENST00000248054]

rs1044880

3'

c

4888

t

6,27E-04

ND

15-LOX-DICE

FK506-binding protein 1A [P20071/ENST00000262925]

 

3'

a

518

g

6,30E-04

ND

 

Epsin 4 [Q14677/ENST00000296951]

rs254682

3'

t

3136

c

6,86E-04

ND

 

40S ribosomal protein S5 [P46782/ENST00000196551]

 

5'

c

27

t

6,94E-04

ND

 

Rho-related GTP-binding protein RhoH [Q15669/ENST00000303700]

rs2245466

5'

g

175

c

6,99E-04

ND

 

Death-associated protein. [Q9BUC9/ENST00000230895]

rs267927

5'

t

163

c

1,69E-03

ND

 

Inhibitor of apoptosis protein 1 [Q13489/ENST00000263464]

 

5'

t

539

g

4,88E-03

ND

 

Kruppel-like factor 6 [Q99612/ENST00000173785]

 

3'

c

1206

t

9,50E-03

ND

 
  1. The Table shows a selection of 50 UTR-SNPs (out of 358) with significantly different allele frequency in normal versus tumoral tissues (exact Fisher's test; p < 0.01). UTR-SNPs are ranked by decreasing p-value. Swissprot protein accession references and Ensembl transcript accession references are indicated between brackets. Candidate positive after the multiple testing corrections are set in italics (Bonferroni), in bold (Benjamini and Hochberg) or underlined (candidate positive after a resampling procedure). Predictive effect of the polymorphisms on RNA secondary structure and putative UTR functional elements is indicated. Asterisk means that the reference allele sequence is modified by the cancer-associated UTR-SNP. For full data access, see Additional file 1. Accession numbers and SNP rs numbers are indicated in column 1 (description) and column 2 (SNP ID), respectively.
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