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Table 2 Associations of susceptibility loci with overall and estrogen receptor-positive and -negative breast cancer a

From: Associations of common breast cancer susceptibility alleles with risk of breast cancer subtypes in BRCA1 and BRCA2 mutation carriers

       

BRCA1 carriers

BRCA2 carriers

        

Overall

 

ER-negative

 

ER-positive

   

Overall

 

ER-negative

 

ER-positive

  

Locus

SNP

Position b

Nearby gene

Ref c

Eff d

K e

MAF

HR (95% CI)

P -value

HR (95% CI)

P -value

HR (95% CI)

P -value

P het-value f

MAF

HR (95% CI)

P -value

HR (95% CI)

P -value

HR (95% CI)

P -value

P het-value f

1p36.22

rs616488

10566215

PEX14

A

G

No

0.32

0.96 (0.92 to 1.01)

0.10

0.95 (0.90 to 1.00)

0.07

1.00 (0.90 to 1.10)

0.92

0.47

0.33

0.98 (0.92 to 1.04)

0.52

1.01 (0.88 to 1.16)

0.94

0.97 (0.9 to 1.05)

0.46

0.69

1p13.2

rs12022378

114448389

SYT6

G

A

No

0.16

1.03 (0.98 to 1.09)

0.25

1.03 (0.97 to 1.10)

0.31

1.03 (0.90 to 1.17)

0.68

0.94

0.17

1.03 (0.95 to 1.12)

0.42

1.16 (0.97 to 1.37)

0.10

1.00 (0.91 to 1.1)

1.00

0.15

1p11.2

rs11249433

121280613

FCGR1B

A

G

Yes

0.41

0.99 (0.95 to 1.04)

0.78

0.99 (0.94 to 1.03)

0.55

1.02 (0.93 to 1.13)

0.63

0.50

0.41

1.05 (0.99 to 1.12)

0.09

1.04 (0.91 to 1.19)

0.57

1.06 (0.99 to 1.13)

0.12

0.84

1q32.1a

rs6678914

202187176

LGR6

G

A

No

0.4

0.98 (0.94 to 1.02)

0.39

0.96 (0.91 to 1.01)

0.08

1.06 (0.97 to 1.17)

0.21

0.07

0.41

1.04 (0.98 to 1.10)

0.19

0.94 (0.82 to 1.08)

0.39

1.07 (1.00 to 1.15)

0.05

0.11

1q32.1b

rs4245739

204518842

MDM4

A

C

Yes

0.28

1.10 (1.05 to 1.15)

4.6 × 10 −5

1.12 (1.07 to 1.19)

1.4 × 10 −5

1.02 (0.91 to 1.13)

0.76

0.11

0.28

0.97 (0.91 to 1.04)

0.38

1.09 (0.95 to 1.26)

0.21

0.94 (0.87 to 1.01)

0.10

0.07

2p24.1

rs12710696

19320803

OSR1

G

A

No

0.39

1.01 (0.97 to 1.06)

0.51

1.01 (0.97 to 1.07)

0.57

1.01 (0.92 to 1.12)

0.77

1.00

0.38

1.00 (0.94 to 1.06)

0.99

1.14 (1.00 to 1.30)

0.05

0.96 (0.9 to 1.03)

0.28

0.02

2q14.2

rs4849887

121245122

 

G

A

No

0.11

1.02 (0.96 to 1.09)

0.53

1.01 (0.94 to 1.09)

0.78

1.05(0.90 to 1.23)

0.49

0.64

0.11

0.98 (0.89 to 1.08)

0.72

1.08 (0.87 to 1.33)

0.49

0.96 (0.85 to 1.07)

0.43

0.34

2q31.1

rs2016394

172972971

DLX2

G

A

No

0.47

1.01 (0.97 to 1.06)

0.54

1.03 (0.98 to 1.08)

0.23

0.96 (0.87 to 1.06)

0.39

0.21

0.46

0.99 (0.93 to 1.05)

0.74

1.07 (0.94 to 1.22)

0.32

0.97 (0.9 to 1.04)

0.36

0.21

2q31.1

rs1550623

174212894

CDCA7

A

G

No

0.15

1.01 (0.95 to 1.07)

0.72

1.02 (0.95 to 1.09)

0.54

0.97 (0.85 to 1.12)

0.72

0.57

0.15

0.97 (0.89 to 1.06)

0.49

1.03 (0.87 to 1.23)

0.70

0.95 (0.87 to 1.05)

0.31

0.41

2q35

rs13387042

217905832

TNP1

A

G

Yes

0.47

0.98 (0.94 to 1.02)

0.41

1.02 (0.97 to 1.07)

0.37

0.86 (0.78 to 0.95)

1.9 × 10 −3

2.3 × 10 −3

0.48

0.99 (0.93 to 1.05)

0.68

0.98 (0.87 to 1.12)

0.82

0.99 (0.93 to 1.06)

0.74

0.96

2q35

rs16857609

218296508

DIRC3

G

A

No

0.26

1.04 (1.00 to 1.09)

0.06

1.03 (0.98 to 1.09)

0.23

1.08 (0.97 to 1.21)

0.14

0.47

0.27

0.96 (0.90 to 1.03)

0.26

0.87 (0.74 to 1.01)

0.08

0.99 (0.92 to 1.07)

0.82

0.14

3p26.1

rs6762644

4742276

ITPR1

A

G

No

0.36

1.04 (0.99 to 1.08)

0.09

1.00 (0.95 to 1.05)

0.92

1.16 (1.05 to 1.28)

2.9 × 10 −3

0.01

0.37

0.98 (0.93 to 1.05)

0.61

1.08 (0.94 to 1.24)

0.27

0.96 (0.89 to 1.03)

0.24

0.13

3p24.1

rs4973768

27416013

SLC4A7

G

A

Yes

0.49

1.01 (0.97 to 1.06)

0.47

0.99 (0.95 to 1.04)

0.81

1.09 (0.99 to 1.19)

0.07

0.10

0.5

1.08 (1.02 to 1.15)

7.8 × 10 −3

1.05 (0.92 to 1.20)

0.46

1.10 (1.02 to 1.18)

0.01

0.58

3p24.1

rs12493607

30682939

TGFBR2

C

G

No

0.35

0.99 (0.95 to 1.04)

0.73

0.99 (0.94 to 1.04)

0.63

1.01 (0.92 to 1.11)

0.85

0.70

0.34

0.98 (0.92 to 1.04)

0.54

1.07 (0.93 to 1.22)

0.35

0.96 (0.89 to 1.03)

0.23

0.17

4q24

rs9790517

106084778

TET2

G

A

No

0.23

0.98 (0.94 to 1.03)

0.51

0.97 (0.92 to 1.03)

0.30

1.03 (0.92 to 1.15)

0.61

0.37

0.22

0.97 (0.91 to 1.05)

0.48

0.91 (0.77 to 1.07)

0.25

0.99 (0.91 to 1.08)

0.88

0.35

4q34.1

rs6828523

175846426

EBF1

C

A

No

0.11

1.03 (0.96 to 1.1)

0.41

1.03 (0.95 to 1.11)

0.47

1.02 (0.88 to 1.19)

0.78

0.94

0.1

0.98 (0.89 to 1.08)

0.72

1.05 (0.85 to 1.30)

0.64

0.96 (0.86 to 1.08)

0.51

0.49

5p15.33

rs10069690

1279790

TERT

G

A

Yes

0.28

1.21 (1.15 to 1.26)

1.1 × 10 −15

1.24 (1.18 to 1.31)

2.7 × 10 −15

1.09 (0.98 to 1.22)

0.09

0.04

0.27

1.11 (1.04 to 1.19)

1.6 × 10 −3

1.25 (1.08 to 1.44)

3.2 × 10 −3

1.08 (1.00 to 1.17)

0.06

0.09

5p15.33

rs7725218

1282414

TERT

G

A

Yes

0.36

1.08 (1.04 to 1.13)

3.2 × 10 −4

1.09 (1.04 to 1.15)

6.4 × 10 −4

1.05 (0.95 to 1.15)

0.37

0.47

0.36

1.06 (0.99 to 1.12)

0.08

1.07 (0.93 to 1.23)

0.35

1.05 (0.98 to 1.13)

0.17

0.85

5p15.33

rs2736108

1297488

TERT

G

A

Yes

0.29

0.89 (0.85 to 0.93)

4.2 × 10 −7

0.86 (0.82 to 0.91)

1.1 × 10 −7

0.98 (0.88 to 1.08)

0.68

0.04

0.3

0.93(0.88 to 1.00)

0.04

0.91 (0.78 to 1.05)

0.20

0.94 (0.87 to 1.02)

0.13

0.67

5p12

rs10941679

44706498

MRPS30

A

G

Yes

0.25

0.99 (0.94 to 1.04)

0.61

0.99 (0.94 to 1.05)

0.84

0.97 (0.86 to 1.08)

0.54

0.66

0.24

1.07 (1.00 to 1.15)

0.03

1.09 (0.94 to 1.27)

0.24

1.07 (0.99 to 1.15)

0.09

0.78

5q11.2

rs889312

56031884

MAP3K1

A

C

Yes

0.29

1.01 (0.97 to 1.06)

0.52

0.99 (0.94 to 1.05)

0.82

1.09 (0.98 to 1.21)

0.12

0.15

0.3

1.04 (0.98 to 1.11)

0.21

0.99 (0.86 to 1.14)

0.90

1.06 (0.98 to 1.14)

0.14

0.44

5q11.3

rs10472076

58184061

RAB3C

A

G

No

0.37

1.00 (0.96 to 1.05)

0.83

0.98 (0.94 to 1.03)

0.52

1.08 (0.98 to 1.18)

0.13

0.11

0.38

0.99 (0.93 to 1.05)

0.78

1.02 (0.89 to 1.17)

0.78

0.98 (0.92 to 1.05)

0.64

0.66

5q11.3

rs1353747

58337481

PDE4D

A

C

No

0.09

0.98 (0.91 to 1.05)

0.53

0.95 (0.88 to 1.04)

0.28

1.06 (0.90 to 1.24)

0.50

0.29

0.09

0.95 (0.86 to 1.05)

0.35

1.02 (0.81 to 1.27)

0.88

0.94 (0.83 to 1.05)

0.26

0.52

5q33.3

rs1432679

158244083

 

A

G

No

0.44

1.05 (1.00 to 1.09)

0.03

1.03 (0.98 to 1.08)

0.25

1.10 (1.01 to 1.21)

0.04

0.21

0.45

1.01 (0.95 to 1.07)

0.79

0.92 (0.81 to 1.04)

0.16

1.04 (0.97 to 1.11)

0.30

0.09

6p25.3

rs11242675

1318878

FOXQ1

A

G

No

0.35

0.96 (0.92 to 1)

0.06

0.94 (0.90 to 0.99)

0.03

1.01 (0.91 to 1.11)

0.90

0.28

0.36

1.01 (0.95 to 1.07)

0.79

1.02 (0.89 to 1.18)

0.75

1.00 (0.93 to 1.08)

0.90

0.83

6p24.3

rs9348512

10456706

TFAP2A

C

A

Yes

0.34

1.00 (0.95 to 1.04)

0.87

1.00 (0.95 to 1.05)

0.88

1.00 (0.90 to 1.10)

0.95

1.00

0.34

0.85 (0.8 to 0.9)

9.2 × 10 −8

0.79 (0.69 to 0.91)

1.1 × 10 −3

0.86 (0.8 to 0.92)

3.4 × 10 −5

0.32

6p23

rs204247

13722523

RANBP9

A

G

No

0.44

1.00 (0.96 to 1.04)

0.98

1.00 (0.95 to 1.04)

0.84

1.01 (0.92 to 1.12)

0.75

0.72

0.44

1.09 (1.03 to 1.15)

3.4 × 10 −3

1.08 (0.94 to 1.24)

0.25

1.09 (1.02 to 1.17)

9.7 × 10 −3

0.93

6q14

rs17530068

82193109

FAM46A

A

G

Yes

0.25

1.03 (0.98 to 1.08)

0.23

1.03 (0.97 to 1.09)

0.29

1.03 (0.92 to 1.14)

0.63

0.95

0.25

1.10 (1.03 to 1.18)

7.2 × 10 −3

1.07 (0.92 to 1.25)

0.40

1.11 (1.02 to 1.2)

0.01

0.70

6q25.1

rs3757318

151914113

ESR1

G

A

Yes

0.08

1.20 (1.11 to 1.29)

1.1 × 10 −6

1.24 (1.14 to 1.35)

5.6 × 10 −7

1.06 (0.89 to 1.26)

0.51

0.12

0.09

1.15 (1.03 to 1.28)

0.01

1.33 (1.07 to 1.65)

9.1 × 10 −3

1.09 (0.96 to 1.24)

0.17

0.12

6q25.1

rs2046210

151948366

ESR1

G

A

Yes

0.37

1.16 (1.12 to 1.21)

2.4 × 10 −12

1.20 (1.15 to 1.26)

2.8 × 10 −13

1.04 (0.94 to 1.15)

0.42

0.01

0.37

1.06 (0.99 to 1.12)

0.07

1.15 (1.00 to 1.33)

0.04

1.03 (0.96 to 1.1)

0.43

0.17

7q35

rs720475

144074929

ARHGEF5

G

A

Yes

0.26

0.98 (0.93 to 1.03)

0.36

0.98 (0.93 to 1.04)

0.54

0.96 (0.86 to 1.08)

0.53

0.79

0.26

0.99 (0.92 to 1.06)

0.71

0.94 (0.80 to 1.09)

0.41

1.00 (0.93 to 1.08)

0.96

0.45

8p12

rs9693444

29509616

DUSP4

C

A

Yes

0.33

1.01 (0.96 to 1.05)

0.80

1.01 (0.96 to 1.06)

0.69

0.99 (0.90 to 1.09)

0.83

0.72

0.33

0.98 (0.93 to 1.05)

0.61

0.92 (0.80 to 1.07)

0.28

1.00 (0.94 to 1.07)

0.94

0.32

8q21.11

rs6472903

76230301

 

A

C

Yes

0.17

1.01 (0.96 to 1.07)

0.74

1.01 (0.95 to 1.08)

0.77

1.01 (0.89 to 1.14)

0.89

0.99

0.16

0.97 (0.90 to 1.05)

0.48

0.95 (0.79 to 1.14)

0.56

0.98 (0.89 to 1.07)

0.66

0.75

8q21.11

rs2943559

76417937

HNF4G

A

G

Yes

0.08

1.06 (0.98 to 1.14)

0.12

1.07 (0.98 to 1.17)

0.12

1.02 (0.86 to 1.22)

0.78

0.68

0.09

1.10 (1.00 to 1.22)

0.05

1.14 (0.91 to 1.43)

0.27

1.09 (0.97 to 1.23)

0.13

0.77

8q24.21

rs11780156

129194641

MYC

G

A

No

0.19

0.95 (0.9 to 1)

0.05

0.96 (0.90 to 1.02)

0.15

0.93 (0.82 to 1.05)

0.23

0.70

0.19

0.97 (0.90 to 1.04)

0.44

0.95 (0.81 to 1.12)

0.56

0.98 (0.9 to 1.06)

0.60

0.79

8q24.21

rs13281615

128355618

 

A

G

Yes

0.43

1.02 (0.98 to 1.06)

0.44

1.01 (0.96 to 1.06)

0.73

1.04 (0.95 to 1.15)

0.38

0.55

0.43

1.03 (0.97 to 1.09)

0.33

1.05 (0.92 to 1.20)

0.44

1.02 (0.96 to 1.1)

0.51

0.71

9p21.3

rs1011970

22062134

CDKN2B

C

A

Yes

0.17

1.02 (0.97 to 1.08)

0.47

1.07 (1.00 to 1.14)

0.05

0.87 (0.76 to 0.99)

0.04

9.3 × 10 −3

0.17

1.03 (0.95 to 1.11)

0.50

1.11 (0.94 to 1.32)

0.21

1.00 (0.92 to 1.1)

0.95

0.29

9q31.2

rs10759243

110306115

KLF4

C

A

No

0.31

0.98 (0.94 to 1.02)

0.39

0.98 (0.93 to 1.03)

0.49

0.98 (0.88 to 1.08)

0.64

0.93

0.29

1.00 (0.94 to 1.06)

0.94

0.94 (0.81 to 1.09)

0.40

1.01 (0.94 to 1.09)

0.69

0.37

9q31.2

rs865686

110888478

KLF4

A

C

Yes

0.36

0.99 (0.95 to 1.04)

0.77

1.02 (0.97 to 1.07)

0.52

0.92 (0.83 to 1.02)

0.11

0.10

0.36

0.99 (0.93 to 1.05)

0.75

1.16 (1.01 to 1.34)

0.04

0.94 (0.88 to 1.01)

0.12

0.01

10p12.31

rs7072776

22032942

MLLT10

G

A

No

0.31

0.99 (0.94 to 1.03)

0.52

0.96 (0.91 to 1.01)

0.11

1.08 (0.98 to 1.20)

0.12

0.04

0.3

0.99 (0.92 to 1.05)

0.67

0.88 (0.77 to 1.02)

0.08

1.02 (0.94 to 1.09)

0.66

0.09

10p12.31

rs11814448

22315843

DNAJC1

A

C

No

0.02

  

1.10 (0.94 to 1.29)

0.22

1.25 (0.93 to 1.69)

0.15

0.50

        

10q21.2

rs10995190

64278682

ZNF365

G

A

Yes

0.15

0.99 (0.93 to 1.05)

0.70

1.02 (0.96 to 1.09)

0.49

0.88 (0.76 to 1.00)

0.06

0.05

0.15

0.94 (0.86 to 1.02)

0.16

0.92 (0.76 to 1.12)

0.43

0.95 (0.86 to 1.04)

0.26

0.84

10q22.3

rs704010

80841148

ZMIZ1

G

A

Yes

0.37

1.01 (0.97 to 1.06)

0.48

0.99(0.94 to 1.04)

0.61

1.12 (1.01 to 1.23)

0.03

0.03

0.38

1.01 (0.95 to 1.07)

0.86

1.02 (0.90 to 1.16)

0.78

1.00 (0.93 to 1.07)

0.96

0.83

10q25.2

rs7904519

114773927

TCF7L2

A

G

Yes

0.47

1.09 (1.05 to 1.14)

1.6 × 10 −5

1.09 (1.04 to 1.14)

6.4 × 10 −4

1.12 (1.02 to 1.23)

0.02

0.59

0.47

1.02 (0.96 to 1.08)

0.56

0.89 (0.78 to 1.01)

0.07

1.06 (0.99 to 1.13)

0.10

0.02

10q26.12

rs2981579

123337335

FGFR2

G

A

Yes

0.42

0.99 (0.95 to 1.04)

0.81

0.92 (0.87 to 0.96)

6.9 × 10 −4

1.29 (1.17 to 1.43)

3.1 × 10 −7

7.5 × 10 −9

0.44

1.24 (1.16 to 1.31)

5.4 × 10 −12

1.05 (0.92 to 1.20)

0.44

1.29 (1.21 to 1.38)

2.2 × 10 −13

7.3 × 10 −3

10q26.12

rs11199914

123093901

FGFR2

G

A

No

0.33

1.02 (0.98 to 1.07)

0.27

1.04 (0.99 to 1.10)

0.09

0.96 (0.86 to 1.06)

0.43

0.17

0.33

0.95 (0.90 to 1.02)

0.15

0.90 (0.78 to 1.03)

0.13

0.97 (0.9 to 1.04)

0.44

0.33

11p15.5

rs3817198

1909006

LSP1

A

G

Yes

0.33

1.08 (1.03 to 1.13)

6.5 × 10 −4

1.08 (1.03 to 1.14)

2.9 × 10 −3

1.07 (0.97 to 1.18)

0.17

0.89

0.34

1.11 (1.04 to 1.18)

9.3 × 10 −4

0.98 (0.85 to 1.13)

0.80

1.15 (1.07 to 1.24)

1.1 × 10 −4

0.06

11q13.1

rs3903072

65583066

SNX32

C

A

No

0.47

0.99 (0.95 to 1.03)

0.69

1.00 (0.95 to 1.05)

0.94

0.96 (0.87 to 1.05)

0.39

0.44

0.47

0.97 (0.91 to 1.03)

0.34

0.89 (0.78 to 1.01)

0.07

1.00 (0.93 to 1.07)

0.91

0.12

11q13.3

rs554219

69331642

CCND1

C

G

Yes

0.12

1.03 (0.97 to 1.09)

0.37

1.00 (0.93 to 1.08)

0.96

1.12 (0.97 to 1.29)

0.12

0.20

0.13

1.09 (1.00 to 1.19)

0.05

0.90 (0.73 to 1.10)

0.31

1.15 (1.04 to 1.26)

5.0 × 10 −3

0.04

11q13.3

c11_pos69088342

69379161

 

C

A

Yes

0.06

1.03 (0.95 to 1.13)

0.45

1.00 (0.90 to 1.12)

0.95

1.14 (0.93 to 1.39)

0.20

0.30

0.06

1.07 (0.95 to 1.21)

0.28

0.85 (0.64 to 1.14)

0.29

1.14 (0.99 to 1.3)

0.08

0.09

11q13.3

rs494406

69344241

 

G

A

Yes

0.25

1.02 (0.97 to 1.07)

0.46

1.02 (0.97 to 1.08)

0.42

1.00 (0.90 to 1.12)

0.97

0.74

0.26

1.05 (0.98 to 1.12)

0.16

1.03 (0.89 to 1.19)

0.66

1.05 (0.98 to 1.14)

0.18

0.80

11q24.3

rs11820646

129461171

BARX2

G

A

No

0.39

0.93 (0.89 to 0.97)

5.9 × 10 −4

0.94 (0.90 to 0.99)

0.03

0.88 (0.79 to 0.97)

8.9 × 10 −3

0.20

0.39

0.92 (0.86 to 0.97)

4.2 × 10 −3

0.95 (0.83 to 1.09)

0.45

0.91 (0.84 to 0.97)

5.9 × 10 −3

0.56

12p13.1

rs12422552

14413931

ATF7IP

G

C

No

0.27

1.01 (0.97 to 1.06)

0.63

1.01 (0.96 to 1.07)

0.68

1.01 (0.91 to 1.13)

0.85

0.99

0.28

1.00 (0.93 to 1.06)

0.92

1.02 (0.88 to 1.19)

0.79

0.99 (0.92 to 1.07)

0.79

0.73

12p11.22

rs10771399

28155080

PTHLH

A

G

Yes

0.10

0.85 (0.80 to 0.91)

1.9 × 10 −6

0.83 (0.77 to 0.9)

1.2 × 10 −5

0.91 (0.78 to 1.06)

0.24

0.36

0.1

0.89 (0.81 to 0.98)

0.02

0.72 (0.56 to 0.91)

6.6 × 10 −3

0.94 (0.84 to 1.05)

0.25

0.05

12q22

rs17356907

96027759

NTN4

A

G

No

0.29

0.95 (0.91 to 1.00)

0.03

0.94 (0.90 to 1.00)

0.03

0.98 (0.88 to 1.09)

0.71

0.56

0.3

0.99 (0.93 to 1.06)

0.78

0.95 (0.83 to 1.10)

0.51

1.00 (0.93 to 1.08)

0.96

0.55

12q24.21

rs1292011

115836522

TBX3

A

G

Yes

0.41

1.00 (0.96 to 1.05)

0.82

1.04 (0.99 to 1.10)

0.08

0.88 (0.80 to 0.97)

0.01

4.39 × 10 −3

0.41

0.92 (0.87 to 0.98)

0.01

1.07 (0.94 to 1.23)

0.29

0.88 (0.82 to 0.95)

5.7 × 10 −4

0.01

13q13.1

rs11571833

32972626

BRCA2

T

A

No

0.01

1.02 (0.83 to 1.26)

0.83

1.05 (0.83 to 1.34)

0.66

0.92 (0.53 to 1.59)

0.75

0.66

0.03

0.95 (0.78 to 1.16)

0.62

0.91 (0.58 to 1.41)

0.66

0.97 (0.78 to 1.2)

0.76

0.80

14q13.3

rs2236007

37132769

PAX9

G

A

No

0.21

0.97 (0.92 to 1.02)

0.19

0.95 (0.90 to 1.01)

0.13

1.01 (0.90 to 1.14)

0.87

0.42

0.21

0.99 (0.92 to 1.07)

0.83

1.20 (1.03 to 1.40)

0.02

0.94 (0.86 to 1.02)

0.13

8.5 × 10 −3

14q24.1

rs2588809

68660428

 

G

A

No

0.19

0.96 (0.91 to 1.01)

0.09

0.95 (0.89 to 1.01)

0.13

0.97 (0.86 to 1.09)

0.56

0.85

0.2

1.01 (0.94 to 1.09)

0.82

0.95 (0.80 to 1.13)

0.55

1.03 (0.94 to 1.12)

0.55

0.44

14q24.1

rs999737

69034682

RAD51L1

G

A

Yes

0.21

0.96 (0.91 to 1.01)

0.09

0.98 (0.92 to 1.04)

0.43

0.90 (0.80 to 1.01)

0.07

0.22

0.22

0.97 (0.91 to 1.05)

0.48

0.95 (0.81 to 1.11)

0.53

0.98 (0.91 to 1.06)

0.65

0.72

14q32.11

rs941764

91841069

CCDC88C

A

G

No

0.34

1.03 (0.98 to 1.07)

0.23

1.02 (0.97 to 1.07)

0.47

1.05 (0.95 to 1.17)

0.34

0.62

0.34

1.03 (0.97 to 1.09)

0.39

1.00 (0.88 to 1.14)

0.97

1.04 (0.97 to 1.11)

0.32

0.61

16q12.1a

rs3803662

52586341

TOX3

G

A

Yes

0.29

1.06 (1.01 to 1.11)

0.02

1.01 (0.96 to 1.07)

0.65

1.22 (1.10 to 1.35)

1.5 × 10 −4

2.39 × 10 −3

0.29

1.24 (1.16 to 1.32)

6.2 × 10 −11

1.12 (0.97 to 1.30)

0.11

1.27 (1.18 to 1.36)

1.5 × 10 −10

0.15

16q12.1b

rs11075995

53855291

FTO

A

T

No

0.24

1.01 (0.96 to 1.06)

0.61

0.98 (0.93 to 1.04)

0.60

1.11 (0.99 to 1.24)

0.07

0.07

0.24

1.02(0.95 to 1.09)

0.59

1.01 (0.86 to 1.18)

0.94

1.02 (0.94 to 1.11)

0.57

0.85

16q12.1b

rs17817449

53813367

FTO

A

C

No

0.41

0.95 (0.91 to 0.99)

0.02

0.94 (0.89 to 0.98)

9.8 × 10 −3

1.00 (0.91 to 1.10)

0.99

0.26

0.41

0.94 (0.88 to 1.00)

0.03

1.05 (0.91 to 1.21)

0.49

0.91 (0.85 to 0.97)

6.6 × 10 −3

0.08

16q23.2

rs13329835

80650805

CDYL2

A

G

No

0.23

1.04 (0.99 to 1.09)

0.09

1.03 (0.97 to 1.09)

0.29

1.08 (0.97 to 1.21)

0.17

0.48

0.24

1.03 (0.96 to 1.11)

0.35

0.94 (0.81 to 1.10)

0.43

1.06 (0.98 to 1.15)

0.13

0.17

17q22

rs6504950

53056471

COX11

G

A

Yes

0.27

0.98 (0.94 to 1.03)

0.49

0.99 (0.94 to 1.04)

0.70

0.96 (0.87 to 1.07)

0.49

0.68

0.27

1.04 (0.97 to 1.11)

0.24

1.08 (0.94 to 1.24)

0.27

1.03 (0.95 to 1.11)

0.46

0.54

18q11.2

rs527616

24337424

AQP4

C

G

No

0.37

0.99 (0.95 to 1.03)

0.61

0.97 (0.93 to 1.02)

0.30

1.04 (0.94 to 1.15)

0.42

0.26

0.37

0.96 (0.9 to 1.02)

0.19

0.95 (0.83 to 1.08)

0.41

0.96 (0.9 to 1.03)

0.30

0.82

18q11.2

rs1436904

22824665

 

A

C

No

0.39

0.99 (0.95 to 1.03)

0.68

1.00 (0.95 to 1.05)

0.86

0.98 (0.89 to 1.08)

0.63

0.74

0.39

0.96 (0.9 to 1.02)

0.14

1.02 (0.89 to 1.17)

0.79

0.94 (0.87 to 1.01)

0.07

0.30

19p13.11

rs8170

17389704

BABAM1

G

A

Yes

0.19

1.19 (1.12 to 1.25)

2.9 × 10 −10

1.22 (1.15 to 1.30)

1.7 × 10 −10

1.06 (0.95 to 1.20)

0.30

0.05

0.19

0.98 (0.91 to 1.06)

0.62

1.06 (0.90 to 1.25)

0.51

0.96 (0.88 to 1.05)

0.37

0.33

19p13.11

rs4808801

18571141

ELL

A

G

No

0.32

0.98 (0.94 to 1.02)

0.40

0.99 (0.94 to 1.05)

0.81

0.94 (0.85 to 1.04)

0.23

0.35

0.33

0.97 (0.91 to 1.03)

0.33

1.07 (0.93 to 1.23)

0.33

0.94 (0.87 to 1.01)

0.10

0.11

19q13.31

rs3760982

44286513

KCNN4

G

A

No

0.46

1.03 (0.99 to 1.08)

0.10

1.03 (0.98 to 1.08)

0.19

1.04 (0.95 to 1.14)

0.41

0.90

0.46

1.05 (0.99 to 1.12)

0.09

0.97 (0.86 to 1.11)

0.69

1.08 (1.01 to 1.15)

0.03

0.19

21q21.1

rs2823093

16520832

NRIP1

G

A

Yes

0.27

0.95 (0.91 to 1)

0.04

0.96 (0.91 to 1.02)

0.17

0.92 (0.82 to 1.02)

0.11

0.44

0.27

0.94 (0.88 to 1.01)

0.09

1.07 (0.92 to 1.25)

0.36

0.91 (0.84 to 0.98)

0.02

0.06

22q12.2

rs132390

29621477

EMID1

A

G

No

0.03

0.98 (0.87 to 1.1)

0.75

0.93 (0.81 to 1.07)

0.30

1.16 (0.91 to 1.46)

0.23

0.13

0.04

1.17 (1.00 to 1.37)

0.05

0.92 (0.61 to 1.39)

0.70

1.24 (1.04 to 1.49)

0.02

0.22

22q13.1

rs6001930

40876234

SGSM3

A

G

No

0.11

1.07 (1.00 to 1.14)

0.03

1.06 (0.98 to 1.15)

0.14

1.11 (0.96 to 1.30)

0.17

0.60

0.10

1.02 (0.92 to 1.12)

0.71

0.94 (0.76 to 1.18)

0.61

1.04 (0.93 to 1.16)

0.48

0.44

  1. aCI, Confidence interval; ER, Estrogen receptor; HR, Hazard ratio; MAF, Mean allele frequency; SNP, Single-nucleotide polymorphism. Results represent BRCA1 and BRCA2 mutation carriers for 74 previously reported breast cancer (BC) susceptibility variants from population-based studies. P-values <0.05 are shown in bold. bPosition in build 37. cReference allele. cEffect allele. eAssociation in BRCA1 and BRCA2 carriers has been reported before. fP-value for the difference between the association with ER-positive BC and the association with ER-negative BC.
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Breast Cancer Research

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