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Table 1 Colorectal cancer risk variants

From: In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants

SNPs

Risk Allele

Locus

Gene(s)

Genomic position

p-value

OR [95%CI]

Reference

rs10911251

A

1q25.3

LAMC1

Intron

2 × 10−8

1.09 [1.06–1.12]

[45, 46]

rs6691170

T

1q41

DUSP10 - HHIPL2

Intergenic

1 × 10−9; 9.6 × 10−10

1.06 [1.03–1.09]; 1.06 [1.03–1.09]

[47, 48]

rs6687758

G

1q41

DUSP10 - HHIPL2

Intergenic

2 × 10−9; 2.3 × 10−9

1.09 [1.06–1.12]; 1.09 [1.06–1.12]

[47, 48]

rs11903757

C

2q32.3

NABP1-SDPR

Intergenic

4 × 10−8

1.16 [1.10–1.22]

[45]

rs35360328

A/T

3p22.1

ZNF621-CTNNB1

Intergenic

3.1 × 10−9

1.14 [1.09–1.19]

[49]

rs812481

G/C

3p14.1

LRIG1

Intron

2 × 10−8

1.09 [1.05–1.11]

[49]

rs10936599

C

3q26.2

MYNN

Synonymous

3 × 10−8; 3.4 × 10−8

1.04 [1.04–1.10]; 0.93 [0.91–0.96]

[48, 50]

rs35509282

A

4q32.2

FSTL5 - NAF1

Intergenic

8.2 × 10−9

1.53 [NR]

[51]

rs367615

?

5q21.3

PJA2-MAN2A1

Intergenic

4 × 10−8

1.35 [1.20–1.49]

[52]

rs647161

A

5q31.1

C5orf66

Intron

1 × 10−10; 4 × 10−10 (East Asian); 1.2 × 10−10

1.11 [1.08–1.15]; 1.17 [1.11–1.22] (East Asian) ; 1.11 [1.08–1.15]

[48, 53]

rs1321311

A

6p21.2

SRSF3-CDKN1A

Intergenic

1 × 10−10; 1.1 × 10−10

1.10 [1.07–1.13]; 1.10 [1.07–1.13]

[48, 54]

rs7758229

T

6q25.3

SLC22A3

Intron

8 × 10−9; 7.9 × 10−9

1.28 [1.18–1.39]; 1.28 [1.18–1.39]

[48, 55]

rs16892766

A

8q23.3

TRPS1-EIF3H

Intergenic

3 × 10−18; 3.3 × 10−18

1.27 [1.20–1.34]; 1.25 [1.19–1.32]

[48, 56]

rs140355816

G

8q23.3

TRPS1-EIF3H

Intergenic

2 × 10−8

1.59 [NR]

[46]

rs10505477

A

8q24.21

FAM84B-POU5F1B

Intron

3.2 × 10−11

1.17 [1.12–1.23]

[48, 57]

rs6983267

G

8q24.21

FAM84B - POU5F1B

ncRNA;intron

1 × 10−11; 7 × 10−11; 1 × 10−14

1.13 [1.09–1.18]; 1.24 [1.17–1.33]; 1.27 I[1.16–1.39]

[45, 48, 55, 56, 58]

rs7014346

A

8q24.21

FAM84B - POU5F1B

Intron

8.6 × 10−26

1.19 [1.14–1.24]

[48, 59]

rs10795668

A

10p14

GATA3-CELF2

Intergenic

3 × 10−13; 2.5 × 10−13

1.12 [1.10–1.16]; 0.89 [0.86–0.91]

[48, 56]

rs11255841

T

10p14

GATA3-CELF2

Intergenic

7 × 10−11

1.19 [NR}

[46]

rs704017

G

10q22.3

RPS24-ZMIZ1

Intergenic

2 × 10−8

1.10 [1.06–1.13]

[22]

rs11190164

G/A

10q24.2

NKX2-3-SLC25A28

Intergenic

4.0 × 10−8

1.09 [1.06–1.12]

[49]

rs1035209

T

10q24.2

NKX2-3-SLC25A28

Intergenic

5 × 10−11

1.12 [1.08–1.16]

[46]

rs12241008

C

10q25

VTI1A

Intron

1.4 × 10−9

1.13 [1.09–1.18]

[60]

rs11196172

A

10q25.2

TCF7L2

Intron

1 × 10−12

1.14 [1.10–1.18]

[22]

rs3824999

C

11q13.4

POLD3

Intron

4 × 10−10; 3.7 × 10−10

1.08 [1.05–1.10]; 0.93 [0.91–0.95]

[48, 54]

rs3802842

C

11q23.1

COLCA2 - COLCA1

Intron

5.8 × 10−10

1.11 [1.08–1.15]

[48, 61]

rs174537

G

11q12.2

MYRF

Intron

9 × 10−21

1.16 [1.12–1.19]

[22]

rs1535

A

11q12.2

FADS2

Intron

8 × 10−20

1.09 [1.04–1.13]

[22]

rs10774214

T

12p13.32

PARP11 - CCND2

Intergenic

3 × 10−8; 5 × 10−10

1.09 [1.06–1.13]; 1.17 [1.11–1.23]

[48, 53]

rs7136702

T

12q13.13

LARP4 - DIP2

Intergenic

4.0 × 10−8

1.06 [1.04–1.08]

[48, 50]

rs10849432

T

12p13.31

CD9- PLEKHG6

Intergenic

6 × 10−10

1.14 [1.09–1.18]

[22]

rs34245511

C

12q13.12

LIMA1

Intron

3 × 10−8

1.14 [NR}

[46]

rs11169552

C

12q13.12

DIP2B - ATF1

Intergenic

2 × 10−10; 1.9 × 10−10

1.09 [1.05–1.11]; 0.92 [0.90–0.95]

[48, 50]

rs3217810

T

12p13.32

CCND2

Intron

2 × 10−10

1.10 [1.06–1.14]

[45, 46]

rs10774214

T

12p13.32

CCND2

Intron

5 × 10−10

1.17 [1.11–1.23]

[53]

rs3184504

C

12q24.12

SH2B3

Missense

1.7 × 10−8

1.09 [1.06–1.12]

[49]

rs73208120

G

12q24.22

NOS1

Intron

2.8 × 10−8

1.16 [1.11–1.23]

[49]

rs4444235

C

14q22.2

DDHD1 - BMP4

Intergenic

8 × 10−10

1.11 [1.08–1.15]

[47, 48, 56]

rs1957636

A

14q22.2

BMP4 - CDKN3

Intergenic

1 × 10−9

1.08 [1.06–1.11]

[62]

rs17094983

A

14q23.1

DACT1 - PRL31P4

Intergenic

2.5 × 10−10

0.87 [0.83–0.91]

[63]

rs4779584

T

15q13.3

SCG5 - GREM1

Intergenic

2 × 10−8; 4.4 × 10 − 14

1.18 [1.11–1.24]; 1.26 [1.19–1.34]

[48, 64]

rs73376930

G

15q13.3

GREM1

Intron

1.0 10−11

1.246 [NR]

[46]

rs9929218

G

16q22.1

CDH1

Intron

1 × 10−8; 1.2 × 10−8

1.10 [1.06–1.12]; 0.91 [0.89–0.94]

[47, 48]

rs12603526

C

17p13.3

NXN

Intron

3 × 10−8

1.10 [1.06–1.14]

[22]

rs7229639

A

18q21.1

SMAD7

Intron

2 × 10−8

1.20 [1.16–1.25]

[22]

rs4939827

T

18q21.1

SMAD7

Intron

2 × 10−10; 8 × 10−28; 1 × 10−12; 1 × 10−12

1.12 [1.09–1.16]; 1.20 [1.16–1.24]; 1.16 [1.09–1.27] ; 0.85 [0.81–0.89]

[48, 61, 64, 65]

rs10411210

C

19q13.11

RHPN2

Intron

5 × 10−9; 4.6 × 10−9

1.15 [1.10–1.20]; 0.87 [0.83–0.91]

[47, 48]

rs1800469

G

19q13.2

TGFB1- B9D2

Intergenic

1 × 10−8

1.09 [1.06–1.12]

[22]

rs961253

A

20p12.3

FERMT1 - BMP2

Intergenic

2 × 10−10

1.12 [1.08–1.16]

[47, 48]

rs2423279

C

20p12.3

BMP2 - HAO1

Intergenic

6.64 × 10−9

1.10 [1.06–1.14]

[48, 53]

rs4813802

G

20p12.3

CASC20 - BMP2

Intergenic

7 × 10-11

1.10 [1.06–1.12]

[62, 64]

rs6066825

G

20q13.1

PREX1

Intron

4.41 × 10−9

1.09 [1.06–1.12]

[49]

rs4925386

C

20q13.33

LAMA5

Intron

2 × 10−10; 1.9 × 10−10

1.08 [1.05–1.10]; 0.93 [0.91–0.95]

[48, 50]

rs2427308

C

20q13.33

CABLES2

Intron

3 × 10−11

1.24 [NR]

[46]

rs5934683

C

Xp22.2

GPR143 - SHROOM2

Intergenic

7.3 × 10−10

1.07 [1.04–1.10]

[48, 54]