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Table 4 Associations with tumor subtypes a

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

         

Affected by subtype, n (MAF)

 

Positive

 

Negative

  

Subtype

Sample

SNP

Locus

Position b

Nearby gene

Ref c

Eff d

Reported e

Positive

Negative

Unknown

Number unaffected (MAF)

HR (95% CI)

P -value

HR (95% CI)

P -value

P het-value f

ER status

BRCA1 carriers

rs10069690

5p15.33

1332790

TERT

G

A

Yes

819 (0.27)

2,635 (0.3)

4,331 (0.3)

7,449 (0.26)

1.09 (0.98 to 1.22)

0.09

1.24 (1.18 to 1.31)

2.7 × 10−15

0.04

  

rs2046210

6q25.1

151990059

C6orf97

G

A

Yes

819 (0.36)

2,639 (0.39)

4,338 (0.38)

7,453 (0.35)

1.04 (0.94 to 1.15)

0.42

1.2 (1.15 to 1.26)

2.8 × 10−13

0.01

  

rs2811708

9p21

21963422

CDKN2A/B

C

A

Yes

816 (0.24)

2,634 (0.31)

4,336 (0.28)

7,445 (0.28)

0.82 (0.73 to 0.91)

2.9 × 10−4

1.13 (1.07 to 1.19)

7.3 × 10−6

3.9 × 10−7

  

rs45631579

10q26

123328965

FGFR2

A

G

Yes

819 (0.48)

2,639 (0.4)

4,337 (0.42)

7,455 (0.41)

1.29 (1.17 to 1.43)

2.6 × 10−7

0.92 (0.87 to 0.96)

4.7 × 10−4

5.1 × 10−9

  

rs2590275

12p12

28057334

PTHLH

G

C

Yes

819 (0.26)

2,639 (0.25)

4,338 (0.26)

7,454 (0.28)

0.92 (0.83 to 1.03)

0.14

0.87 (0.82 to 0.92)

5.3 × 10−7

0.34

  

rs2363956

19p13.11

17255124

ANKLE1

C

A

Yes

819 (0.47)

2,635 (0.53)

4,334 (0.52)

7,447 (0.48)

0.98 (0.89 to 1.08)

0.71

1.25 (1.19 to 1.31)

6.4 × 10−20

1.6 × 10−5

 

BRCA2 carriers

rs2162540

10q26

123342126

FGFR2

A

G

Yes

1450 (0.47)

426 (0.41)

2,348 (0.44)

3,783 (0.38)

1.34 (1.25 to 1.43)

3.6 × 10−16

1.08 (0.94 to 1.23)

0.27

6.1 × 10−3

  

rs17271951

16q12.1

51095541

TOX3

A

G

Yes

1490 (0.32)

434 (0.28)

2,397 (0.3)

3,879 (0.25)

1.29 (1.2 to 1.39)

8.4 × 10−12

1.14 (0.99 to 1.31)

0.08

0.14

PR status

BRCA1 carriers

rs10069690

5p15.33

1332790

TERT

G

A

Yes

662 (0.27)

2,481 (0.29)

4,642 (0.3)

7,449 (0.26)

1.10 (0.98 to 1.24)

0.09

1.24 (1.17 to 1.3)

1.3 × 10−14

0.11

  

rs2046210

6q25.1

151990059

C6orf97

G

A

Yes

662 (0.37)

2,485 (0.39)

4,649 (0.38)

7,453 (0.35)

1.09 (0.98 to 1.21)

0.12

1.18 (1.13 to 1.24)

2.0 × 10−11

0.19

  

rs45631626

10q26

123327325

FGFR2

G

A

Yes

662 (0.49)

2,485 (0.4)

4,647 (0.42)

7,455 (0.42)

1.33 (1.2 to 1.48)

1.3 × 10−7

0.92 (0.88 to 0.97)

9.6 × 10−4

5.3 × 10−9

  

rs2590275

12p12

28057334

PTHLH

G

C

Yes

662 (0.26)

2,485 (0.25)

4,649 (0.26)

7,454 (0.28)

0.92 (0.82 to 1.03)

0.16

0.87 (0.82 to 0.92)

8.2 × 10−7

0.45

  

rs8100241

19p13.11

17253894

ANKLE1

G

A

Yes

657 (0.51)

2,473 (0.47)

4,628 (0.48)

7,420 (0.52)

0.98 (0.88 to 1.09)

0.71

0.81 (0.78 to 0.85)

1.8 × 10−17

2.4 × 10−3

 

BRCA2 carriers

rs10017576

4q28.3

139799629

 

G

A

No

1099 (0.38)

591 (0.43)

2,639 (0.41)

3,880 (0.43)

0.83 (0.77 to 0.89)

8.9 × 10−7

1.02 (0.92 to 1.14)

0.67

2.7 × 10−3

  

rs4376461

8p12

32822117

NRG1

C

A

No

1099 (0.15)

591 (0.10)

2,640 (0.14)

3,881 (0.15)

1.00 (0.9 to 1.12)

0.93

0.6 (0.5 to 0.73)

2.4 × 10−7

1.4 × 10−5

  

rs45631588

10q26

123341292

FGFR2

A

G

Yes

1099 (0.47)

591 (0.43)

2,640 (0.45)

3,881 (0.39)

1.33 (1.23 to 1.44)

2.7 × 10−13

1.15 (1.03 to 1.28)

0.01

0.04

  

rs17271951

16q12.1

51095541

TOX3

A

G

Yes

1099 (0.32)

591 (0.28)

2,631 (0.3)

3,879 (0.25)

1.32 (1.21 to 1.43)

4.3 × 10−11

1.14 (1.01 to 1.29)

0.03

0.07

HER2 status

BRCA1 carriers

rs17008885

2p13.2

73303647

SMYD5

T

A

No

182 (0.19)

1,816 (0.3)

5,799 (0.3)

7,455 (0.31)

0.54 (0.43 to 0.69)

7.8 × 10−7

0.99 (0.95 to 1.04)

0.78

3.8 × 10−6

  

rs10069690

5p15.33

1332790

TERT

G

A

Yes

181 (0.23)

1,813 (0.29)

5,791 (0.3)

7,449 (0.26)

0.9 (0.71 to 1.13)

0.36

1.24 (1.18 to 1.3)

3.4 × 10−17

0.01

  

rs2046210

6q25.1

151990059

C6orf97

G

A

Yes

182 (0.39)

1,816 (0.4)

5,798 (0.38)

7,453 (0.35)

1.12 (0.91 to 1.38)

0.29

1.17 (1.11 to 1.22)

1.5 × 10−10

0.71

  

rs10843055

12p12

28063088

PTHLH

A

C

Yes

171 (0.06)

1,743 (0.06)

5,615 (0.06)

7,234 (0.07)

0.79 (0.52 to 1.2)

0.26

0.79 (0.72 to 0.87)

6.2 × 10−7

0.99

  

rs4808616

19p13.11

17264033

ANKLE1

C

A

Yes

176 (0.35)

1,782 (0.32)

5,706 (0.32)

7,339 (0.28)

1.37 (1.11 to 1.69)

3.8 × 10−3

1.2 (1.14 to 1.26)

6.8 × 10−13

0.25

 

BRCA2 carriers

rs4305889

8q12.1

60352785

TOX

A

G

No

121 (0.18)

845 (0.09)

3,353 (0.11)

3,874 (0.1)

2.04 (1.53 to 2.71)

8.7 × 10−7

0.96 (0.85 to 1.08)

0.47

1.0 × 10−5

  

rs45631588

10q26

123341292

FGFR2

A

G

Yes

121 (0.45)

847 (0.46)

3,362 (0.45)

3,881 (0.39)

1.27 (0.98 to 1.63)

0.07

1.28 (1.19 to 1.37)

2.1 × 10−12

0.95

  

rs3817197

11p15.5

1862750

LSP1

G

A

Yes

121 (0.55)

847 (0.44)

3,353 (0.45)

3,877 (0.47)

1.30 (1.02 to 1.64)

0.03

0.84 (0.79 to 0.9)

9.1 × 10−7

1.3 × 10−3

  

rs17271951

16q12.1

51095541

TOX3

A

G

Yes

121 (0.29)

847 (0.31)

3,353 (0.3)

3,879 (0.25)

1.10 (0.85 to 1.41)

0.47

1.27 (1.18 to 1.37)

6.9 × 10−11

0.3

Triple-negativeg

BRCA1 carriers

rs10069690

5p15.33

1332790

TERT

G

A

Yes

579 (0.27)

1,307 (0.3)

5,899 (0.3)

7,449 (0.26)

1.06 (0.94 to 1.19)

0.34

1.27 (1.2 to 1.36)

5.2 × 10−14

0.02

  

rs2046210

6q25.1

151990059

C6orf97

G

A

Yes

580 (0.37)

1,310 (0.41)

5,906 (0.38)

7,453 (0.35)

1.01 (0.91 to 1.13)

0.79

1.23 (1.16 to 1.31)

5.5 × 10−12

6.8 × 10−3

  

rs9512729

13q12.2

26974865

LNX2

G

A

No

580 (0.34)

1,309 (0.43)

5,902 (0.41)

7,454 (0.41)

0.76 (0.69 to 0.85)

9.1 × 10−7

1.08 (1.02 to 1.15)

0.01

1.2 × 10−6

  

rs8100241

19p13.11

17253894

ANKLE1

G

A

Yes

577 (0.5)

1,304 (0.46)

5,877 (0.48)

7,420 (0.52)

0.94 (0.85 to 1.04)

0.22

0.81 (0.76 to 0.86)

2.4 × 10−13

0.03

 

BRCA2 carriers

rs2162540

10q26

123342126

FGFR2

A

G

Yes

735 (0.46)

133 (0.36)

3,356 (0.44)

3,783 (0.38)

1.39 (1.29 to 1.49)

9.8 × 10−20

0.83 (0.67 to 1.03)

0.10

4.0 × 10−5

  

rs1362548

16q12.1

51121452

TOX3

C

G

Yes

760 (0.32)

136 (0.29)

3,434 (0.31)

3,881 (0.26)

1.26 (1.17 to 1.36)

1.0 × 10−9

1.18 (0.94 to 1.49)

0.16

0.63

  1. aCI, Confidence interval; HR, Hazard ratio; MAF, Mean allele frequency. Single-nucleotide polymorphisms (SNPs) associated at P <10−6 with breast cancer by tumor estrogen receptor (ER) status, progesterone receptor (PR) status, human epidermal growth factor receptor 2 (HER2) status or triple-negative (negative for ER, PR and HER2) are shown. The most strongly associated SNP from each locus is reported. bPosition in build 36. cReference allele. dEffect allele. eVariant located in previously reported breast cancer susceptibility locus. fP-value for the difference in association between subtype positive and subtype negative breast cancer (for example, ER-positive vs ER-negative). gNon–triple negative was considered as “positive” and triple-negative as “negative.”