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Table 2 Associations between susceptibility SNPs and colorectal cancer risk in previously published GWAS and current study

From: Evaluation of gene-environment interactions for colorectal cancer susceptibility loci using case-only and case-control designs

SNP

Chromosomal region

Mapped genea

Alleleb

Previously published study

Current study

RAFc

OR

(95% CI)d

Pd

Reference (study population)

RAFc

PHWEc

OR

(95% CI)d

Pd

A1

A2

rs6687758

1q41

intergenic

G

A

0.20–0.28

1.09

(1.06–1.12)

2.3 × 10−09

Houlston et al. Nat Genet. 2010 (European)

0.27

0.43

1.14

(0.98–1.33)

0.09

rs10936599

3q26.2

MYNN

T

C

0.20–0.26

0.93

(0.91–0.96)

3.4 × 10−08

Houlston et al. Nat Genet. 2010 (European)

0.61

0.22

1.02

(0.89–1.16)

0.78

rs647161

5q31.1

C5orf66

A

C

0.31

1.17

(1.11–1.22)

3.8 × 10−10

Jia et al. Nat Genet. 2012 (East Asian)

0.29

0.94

1.22

(1.09–1.45)

1.5 × 10−03

rs7758229

6q25.3

SLC22A3

T

G

0.22

1.28

(1.18–1.39)

7.9 × 10−09

Cui et al. Gut. 2011 (East Asian)

0.21

0.14

1.08

(0.92–1.26)

0.37

rs6983267

8q24.21

CASC8, CCAT2

G

T

0.49

1.21

(1.15–1.27)

1.3 × 10− 14

Tomlinson et al. Nat Genet. 2007 (European)

0.43

0.22

1.20

(1.06–1.37)

5.0 × 10−03

rs7014346

8q24.21

CASC8

A

G

0.18

1.19

(1.15–1.23)

8.6 × 10−26

Tenesa et al. Nat Genet. 2008 (European)

0.29

0.79

1.16

(1.01–1.34)

0.03

rs10505477

8q24.21

CASC8

A

G

0.50

1.17

(1.12–1.23)

3.2 × 10−11

Zanke et al. Nat Genet. 2007 (European)

0.42

0.16

1.21

(1.07–1.38)

3.5 × 10−03

rs10795668

10p14

LOC105376400

A

G

0.33

0.89

(0.86–0.91)

2.5 × 10−13

Tomlinson et al. Nat Genet. 2008 (European)

0.39

0.73

0.85

(0.74–0.97)

0.02

rs704017

10q22.3

ZMIZ1-AS1

G

A

0.32

1.10

(1.06–1.13)

2.1 × 10−08

Zhang et al. Nat Genet. 2014 (East Asian)

0.34

0.38

1.17

(1.02–1.34)

0.02

rs11196172

10q25.2

TCF7L2

A

G

0.68

1.14

(1.10–1.18)

1.0 × 10−12

Zhang et al. Nat Genet. 2014 (East Asian)

0.73

0.52

1.21

(1.04–1.41)

0.01

rs1665650

10q26.2

HSPA12A

T

C

0.32

1.13

(1.08–1.19)

8.6 × 10−07

Jia et al. Nat Genet. 2012 (East Asian)

0.33

0.13

0.94

(0.81–1.08)

0.38

rs174537

11q12.2

MYRF

G

T

0.59

1.16

(1.12–1.19)

9.2 × 10−21

Zhang et al. Nat Genet. 2014 (East Asian)

0.67

0.72

1.23

(1.07–1.42)

4.1 × 10−03

rs174550

11q12.2

FADS1

T

C

0.59

1.15

(1.12–1.19)

1.6 × 10−19

Zhang et al. Nat Genet. 2014 (East Asian)

0.67

0.67

1.19

(1.04–1.37)

0.01

rs1535

11q12.2

FADS2

A

G

0.59

1.15

(1.12–1.19)

8.2 × 10−20

Zhang et al. Nat Genet. 2014 (East Asian)

0.68

0.86

1.20

(1.04–1.38)

0.01

rs3802842

11q23.1

COLCA1, COLCA2

C

A

0.43

1.11

(1.08–1.15)

5.8 × 10− 10

Tenesa et al. Nat Genet. 2008 (East Asian)

0.41

0.13

1.02

(0.89–1.16)

0.79

rs10849432

12p13.31

intergenic

T

C

0.82

1.14

(1.09–1.18)

5.8 × 10− 10

Zhang et al. Nat Genet. 2014 (East Asian)

0.82

0.66

1.13

(0.95–1.34)

0.17

rs10774214

12p13.32

CCND2-AS1

T

C

0.35

1.17

(1.11–1.23)

5.5 × 10−10

Jia et al. Nat Genet. 2012 (East Asian)

0.42

0.84

1.08

(0.95–1.23)

0.25

rs11169552

12q13.13

ATF1, LOC105369765

T

C

0.23–0.26

0.92

(0.90–0.95)

1.9 × 10−10

Houlston et al. Nat Genet. 2010 (European)

0.33

0.51

1.03

(0.90–1.18)

0.71

rs7136702

12q13.13

intergenic

T

C

0.32–0.39

1.06

(1.04–1.08)

4.0 × 10−08

Houlston et al. Nat Genet. 2010 (European)

0.52

0.04

1.03

(0.90–1.18)

0.65

rs4444235

14q22.2

intergenic

C

T

0.46

1.11

(1.08–1.15)

8.1 × 10−10

Houlston et al. Nat Genet. 2008 (European)

0.52

0.52

1.02

(0.90–1.15)

0.80

rs1957636

14q22.3

LOC105370507

A

G

0.38–0.43

1.08

(1.06–1.11)

1.4 × 10−09

Tomlinson et al. PLoS Genet. 2011 (European)

0.60

0.74

0.90

(0.79–1.02)

0.11

rs4779584

15q13.3

intergenic

Ae

Ge

0.19

1.18

(1.11–1.24)

1.8 × 10−08

Peters et al. Hum Genet. 2011 (European)

0.84

0.91

1.21

(1.00–1.46)

0.05

rs9929218

16q22.1

CDH1

Ae

Ge

0.29

0.91

(0.89–0.94)

1.2 × 10−08

Houlston et al. Nat Genet. 2008 (European)

0.15

0.47

1.11

(0.93–1.33)

0.24

rs12603526

17p13.3

NXN

C

T

0.30

1.10

(1.06–1.14)

3.4 × 10−08

Zhang et al. Nat Genet. 2014 (East Asian)

0.36

0.93

0.96

(0.84–1.10)

0.53

rs4939827

18q21.1

SMAD7

C

T

0.48

0.85

(0.81–0.89)

1.0 × 10−12

Broderick et al. Nat Genet. 2007 (European)

0.78

0.10

0.86

(0.74–1.01)

0.06

rs10411210

19q13.11

RHPN2

T

C

0.10

0.87

(0.83–0.91)

4.6 × 10−09

Houlston et al. Nat Genet. 2008 (European)

0.21

0.03

0.73

(0.62–0.86)

2.0 × 10−04

rs1800469

19q13.2

B9D2, TGFB1

G

A

0.48

1.09

(1.06–1.12)

1.2 × 10−08

Zhang et al. Nat Genet. 2014 (East Asian)

0.51

0.39

1.04

(0.92–1.19)

0.53

rs2241714

19q13.2

B9D2, TMEM91

C

T

0.48

1.09

(1.06–1.12)

1.4 × 10−08

Zhang et al. Nat Genet. 2014 (East Asian)

0.51

0.38

1.04

(0.92–1.18)

0.55

rs961253

20p12.3

Intergenic

A

C

0.36

1.12

(1.08–1.16)

2.0 × 10−10

Houlston et al. Nat Genet. 2008 (European)

0.09

0.97

1.22

(0.99–1.51)

0.07

rs4813802

20p12.3

Intergenic

G

T

0.34–0.38

1.09

(1.06–1.12)

7.5 × 10−11

Tomlinson et al. PLoS Genet. 2011 (European)

0.21

0.81

1.05

(0.89–1.23)

0.58

rs2423279

20p12.3

intergenic

C

T

0.30

1.14

(1.08–1.19)

2.3 × 10−07

Jia et al. Nat Genet. 2012 (East Asian)

0.27

0.90

1.19

(1.04–1.37)

0.01

  1. SNP single-nucleotide polymorphism, GWAS genome-wide association study, RAF risk/effect allele frequency, OR odds ratio, CI confidence interval
  2. aMapped gene was based on the NCBI dbSNP
  3. bA1 and A2 were respectively designated as risk/effect and reference allele based on the literature
  4. cRAF and PHWE were assessed in controls
  5. dUnadjusted logistic regression analysis based on additive model
  6. eAlleles T instead of A and C instead of G were presented for rs4779584 and rs9929218 in the current study
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