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Table 1 Genetic variants with suggestive (Pint ≤ 5E−07) GxE interactions for overall and estrogen receptor positive (ER +) breast cancer risk

From: A genome-wide gene-environment interaction study of breast cancer risk for women of European ancestry

Risk factor

SNP

Chr

Position1

Alleles2

EAF3

ORmarg

(95% CI)

Pmarg

ORint

(95% CI)

Pint

BFDP4

Overall breast cancer risk

Number of full-term pregnancies (per 1 birth)

rs10928872

2

129,833,111

A/T

0.08

1.00

(0.97–1.03)

0.97

0.93

(0.91–0.96)

1.34E-07

0.98

Number of full-term pregnancies (per 1 birth)

rs36064687

2

129,832,988

AT/A

0.08

1.00

(0.97–1.04)

0.99

0.93

(0.91–0.96)

1.34E-07

0.98

Number of full-term pregnancies (per 1 birth)

rs79929694

2

129,841,483

A/G

0.08

1.00

(0.96–1.03)

0.96

0.93

(0.91–0.96)

1.43E-07

0.98

Number of full-term pregnancies (per 1 birth)

rs77107485

2

129,843,663

T/G

0.08

1.00

(0.97–1.04)

0.89

0.93

(0.91–0.96)

2.79E-07

0.98

Number of full-term pregnancies (per 1 birth)

rs79722231

2

129,834,483

T/C

0.08

1.00

(0.97–1.04)

0.92

0.93

(0.91–0.96)

2.80E-07

0.98

Age at menarche (per 2 years)

rs73277506

7

21,112,413

C/T

0.02

1.03

(0.96–1.10)

0.39

1.26

(1.16–1.38)

1.46E-07

0.75

Current smoking (yes/no)

rs11322161

8

105,120,195

GC/G

0.29

1.00

(0.98–1.02)

0.63

1.19

(1.12–1.27)

9.26E-08

0.49

Adult height (per 5 cm)

rs80018847

9

28,326,896

A/G

0.14

1.00

(0.98–1.03)

0.88

0.94

(0.92–0.96)

4.34E-08

0.11

Adult height (per 5 cm)

rs1360506

9

28,339,154

G/C

0.16

1.00

(0.97–1.03)

0.96

0.95

(0.93–0.98)

2.13E-07

1.00

Adult height (per 5 cm)

rs1237669

17

41,912,024

T/G

0.91

1.01

(0.98–1.04)

0.62

0.94

(0.91–0.96)

5.00E-07

0.16

OC use (yes/no)

rs147290549

18

7,713,860

C/T

0.50

1.01

(0.99–1.02)

0.23

1.10

(1.06–1.14)

4.55E-07

0.59

OC use (yes/no)

rs664040

18

7,716,250

C/A

0.50

1.01

(0.99–1.02)

0.22

1.10

(1.06–1.14)

4.93E-07

0.59

Current smoking

(yes/no)

rs75489324

21

26,302,665

G/C

0.02

0.98

(0.92–1.05)

0.87

0.58

(0.47–0.72)

4.58E-07

0.94

ER + breast cancer risk

Age at menarche (per 2 years)

rs73277506

7

21,112,413

C/T

0.02

1.04

(0.97–1.12)

0.25

1.28

(1.17–1.41)

3.94E-07

0.76

Current smoking (yes/no)

rs11322161

8

105,120,195

GC/G

0.29

1.00

(0.98–1.02)

0.95

1.20

(1.12–1.29)

4.32E-07

0.81

Age at menarche (per 2 years)

rs4770552

13

24,594,430

C/T

0.86

1.02

(1.00–1.05)

0.10

0.91

(0.88–0.94)

4.62E-08

0.11

Age at menarche (per 2 years)

rs113684695

13

24,600,947

ACCTCGT

GATCCGC/A

0.86

1.02

(1.00–1.05)

0.11

0.91

(0.88–0.94)

5.48E-08

0.11

Age at menarche (per 2 years)

rs9510997

13

24,592,857

G/T

0.86

1.02

(1.00–1.05)

0.10

0.91

(0.88–0.94)

6.26E-08

0.11

Age at menarche (per 2 years)

rs7321200

13

24,593,519

A/G

0.87

1.01

(0.99–1.04)

0.33

0.91

(0.87–0.94)

7.92E-08

0.11

Age at menarche (per 2 years)

rs4770553

13

24,595,995

C/T

0.85

1.02

(0.99–1.04)

0.22

0.92

(0.89–0.95)

4.31E-07

0.76

Age at menarche (per 2 years)

rs9551041

13

24,601,810

A/G

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.58E-07

0.76

Age at menarche (per 2 years)

rs1886805

13

24,602,494

G/A

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.62E-07

0.76

Age at menarche (per 2 years)

rs4770555

13

24,601,751

T/C

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.63E-07

0.76

Age at menarche (per 2 years)

rs4770556

13

24,601,760

A/G

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.68E-07

0.76

Age at menarche (per 2 years)

rs1886804

13

24,602,174

T/G

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.72E-07

0.76

Age at menarche (per 2 years)

rs1886803

13

24,602,165

T/C

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.72E-07

0.76

Age at menarche (per 2 years)

rs9553145

13

24,602,061

G/C

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.75E-07

0.76

Age at menarche (per 2 years)

rs4769305

13

24,592,448

T/C

0.85

1.02

(0.99–1.05)

0.17

0.92

(0.89–0.95)

4.76E-07

0.76

Age at menarche (per 2 years)

rs9553144

13

24,601,943

C/G

0.85

1.02

(0.99–1.04)

0.21

0.92

(0.89–0.95)

4.78E-07

0.76

Number of full-term pregnancies (per 1 birth)

rs930198

23

79,492,077

T/C

0.24

1.00

(0.98–1.02)

0.93

0.96

(0.94–0.97)

3.10E-07

0.99

  1. SNP: Single Nucleotide Polymorphism; Chr: Chromosome; Ref: Reference Allele; Alt: Alternative Allele; EAF: Effect Allele Frequency; ORmarg: SNP Marginal Odds ratio; CI: Confidence Interval; Pmarg: Marginal p-value (meta-analyzed); ORint: Interaction p-value (meta-analyzed); Pint: Interaction p-value; BFDP: Bayesian False Discovery Probability; ABF: Approximate Bayes Probability; OC use: Ever use of oral contraceptives; ER + : Estrogen receptor positive breast cancer risk
  2. 1Build 37 Position
  3. 2Reference/Alternate alleles in Europeans (forward strand)
  4. 3Effect allele frequency in controls in OncoArray dataset
  5. 4Bayesian False Discovery Probability at prior probability of 1 × 10–05
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Breast Cancer Research

ISSN: 1465-542X

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