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Table 3 Extended information on SNPs identified in the major GWAS for breast cancer risk or SNPs used to generate published polygenic risk scores

From: Common breast cancer risk variants in the post-COGS era: a comprehensive review

SNPa

Cyto-band

Gene/HGVS designation if applicableb

Breast cancer risk in first reported publication

RAF (EA)

Additional populations studied (other than EA)c

PRSd

References

A

B

C

D

rs11249433

1p11.2

Intergenic

1.16 (1.09 to 1.24)

0.39

A, ER+

*

*

*

 

[30, 32, 35–38]

rs11552449

1p13.2

DCLRE1B p.His61Tyr

1.08 (1.02 to 1.14)

0.17

     

[35]

rs616488

1p36.22

PEX14 c.84 + 10837A > G

0.94 (0.90 to 0.98)

0.33

ER–

    

[35, 39]

rs6678914

1q32.1

LGR6 c.213-7375G > A

1.10 (1.06 to 1.13)

0.59

ER– only

    

[39]

rs2290854

1q32.1

MDM4 c.903 + 20A > G

1.13 (1.08 to 1.18)

0.33

B1+ only

    

[40]

rs4245739

1q32.1

MDM4 c.*32C > A

1.14 (1.10 to 1.18)

0.26

ER– only

    

[39]

rs6682208

1q32.1

Intergenic

1.12 (1.07 to 1.17)

0.34

B1+ only

    

[40]

rs184577

2p22.2

CYP1B1 antisense

0.85 (0.79 to 0.91)

 

B2+ only

    

[41]

rs12710696

2p24.1

Intergenic

1.10 (1.06 to 1.13)

0.36

ER– only

    

[39]

rs4849887

2q14.2

Intergenic

0.90 (0.84 to 0.96)

0.10

AA

    

[35, 42]

rs2016394

2q31.1

Intergenic

0.95 (0.92 to 0.99)

0.48

     

[35]

rs1550623

2q31.1

Intergenic

0.91 (0.86 to 0.96)

0.16

     

[35]

rs1045485 e

2q33.1

CASP8 p.Asp302His

0.89 (0.85 to 0.93)

0.13

AA e

 

*

*

*

[23, 24, 32, 35, 42, 43]

rs17468277f

2q33.1

ALS2CR12 c.1191G > A

0.83 (0.70 to 0.98)

0.09

 

*

   

[44]

rs13387042

2q35

Intergenic

1.20 (1.14 to 1.26)

0.50

H, Ag, AA, B1 + g

*

*

*

*

[27, 30, 32, 33, 35, 40, 42, 45–50]

rs16857609

2q35

DIRC3 noncoding transcript

1.09 (1.05 to 1.14)

0.26

A, ER–

    

[35, 37, 39]

rs4973768

3p24.1

SLC4A7 c.*2242G > A

1.11 (1.08 to 1.13)

0.46

A, B2+

*

*

  

[31–33, 35, 37, 41, 47, 48, 51, 52]

rs12493607

3p24.1

TGFBR2 c.95-3300G > C

1.04 (1.00 to 1.09)

0.35

     

[35]

rs6762644

3p26.1

ITPR1 c.4509 + 651A > G

1.06 (1.02 to 1.11)

0.4

     

[35]

rs9790517

4q24

TET2 c.-193 + 17535C > T

1.09 (1.04 to 1.14)

0.23

     

[35]

rs6828523

4q34.1

ADAM29 c.-450-5711C > A

0.89 (0.83 to 0.94)

0.13

     

[35, 37]

rs4415084f

5p12

Intergenic

1.16 (1.10 to 1.21)

0.40

B1 + f

*

*

  

[28, 53]

rs10941679

5p12

Intergenic

1.19 (1.13 to 1.26)

0.24

AA, A, B2 + e

*

*

  

[30, 32, 33, 35, 37, 47, 50, 54],[55]

rs7716600f

5p12

Intergenic, 54 kb 3′-MRPS30

1.24 (1.14 to 1.34)

0.23

A

  

*

 

[56]

rs10069690

5p15.33

TERT c.1951-205G > A

1.18 (1.13 to 1.25)

0.27

AA, ER+, ER–, B1+

 

*

  

[35, 42, 57–59]

rs16886113

5q11.2

Intergenic, 5′ to MAP3K1

1.24 (1.11 to 1.38)

0.06

B2+ only

    

[41]

rs889312

5q11.2

Intergenic, 5′ to MAP3K1

1.13 (1.10 to 1.16)

0.28

A

*

*

*

*

[25, 32, 35, 37, 48, 56, 60–62]

rs10472076

5q11.2

Intergenic, 5′ to MAP3K1

1.06 (1.02 to 1.11)

0.38

     

[35]

rs1353747

5q11.2

PDE4D c.809-2683A > C

0.90 (0.84 to 0.96)

0.10

     

[35]

rs1432679

5q33.3

EBF1 c.778 + 6101G > A

1.06 (1.02 to 1.10)

0.43

A, ER–

    

[35, 37, 39]

rs204247

6p23

Intergenic (11 kb 5′-RANBP9)

1.06 (1.02 to 1.10)

0.43

     

[35]

rs9348512

6p24.3

Intergenic

0.85 (0.80 to 0.90)

 

B2+ only

    

[41]

rs11242675

6p25.3

Intergenic (3.9 kb 3′-FOXQ1)

0.97 (0.93 to 1.01)

0.39

A

    

[35, 37]

rs17530068

6q14.1

Intergenic

1.12 (1.08 to 1.16)

0.22

AA, ER–

    

[35, 39, 63]

rs6569479f

6q22.33

RNF146 c.3-1173 T > C

1.39 (1.23 to 1.57)

0.21

AJ

 

*

  

[64, 65]

rs2253407

6q25.1

SYNE1 c.23020-466C > A

0.92 (0.86 to 0.98)

0.47

B2+ only

    

[41]

rs9485372

6q25.1

Intergenic, 5′ tp TAB2

0.89 (0.84 to 0.94)

 

A only

    

[37]

rs3757318

6q25.1

CCDC170 c.1294-129G > A

1.30 (1.17 to 1.46)

0.07

ER-

*

*

  

[29, 32, 33, 35, 37–40, 48, 66–69]

rs2046210

6q25.1

Intergenic, 6 kb 3'- CCDC170

1.29 (1.21 to 1.37)

0.35

A, ER–, B1+

*

*

  

rs9383938f

6q25.1

Intergenic, 5′ to ESR1

1.18 (1.10 to 1.27)

0.08

  

*

  

[33, 70]

rs720475

7q35

ARHGEF5 c.4531 + 646G > A

0.93 (0.89 to 0.98)

0.25

     

[35]

rs9693444

8p21

Intergenic

1.07 (1.03 to 1.12)

0.32

A

    

[35, 37]

rs6472903

8q21.11

Intergenic

0.88 (0.84 to 0.93)

0.18

A

    

[35, 37]

rs2943559

8q21.11

HNF4G c.-24 + 15494A > G

1.17 (1.09 to 1.26)

0.07

ER–

    

[35, 39]

rs4733664

8q24.21

Intergenic

1.10 (1.04 to 1.17)

0.41

B2+ only

    

[41]

rs13281615

8q24.21

Intergenic

1.08 (1.05 to 1.11)

0.40

 

*

*

*

*

[25, 33, 35, 47, 71–73]

rs1562430

8q24.21

Intergenic

0.84 (0.78 to 0.90)

0.40

  

*

  

[32, 56]

rs11780156

8q24.21

Intergenic (32 kb 3′-MIR1208)

1.13 (1.07 to 1.19)

0.16

     

[35]

rs10965163

9p21.3

MTAP c.561C > T

0.84 (0.77 to 0.93)

0.10

B2+ only

    

[41]

rs1011970

9p21.3

CDK2NB antisense RNA

1.09 (1.04 to 1.14)

0.17

ER–

*

*

  

[32, 35, 39, 41, 74]

rs865686

9q31.2

Intergenic

0.90 (0.86 to 0.96)

0.39

AA, ER+

*

*

  

[33, 35, 41, 74–76]

rs10759243

9q31.2

Intergenic (53 kb 5′-KLF4)

1.07 (1.02 to 1.12)

0.39

A

    

[35]

rs7072776

10p12.31

Intergenic (382 bp 3′-MLLT10)

1.11 (1.07 to 1.16)

0.29

     

[35]

rs11814448

10p12.31

Intergenic (23 kb 5′-DNAJC1)

1.35 (1.17 to 1.56)

0.02

     

[35]

rs2380205 e

10p15.1

Intergenic , 2.6 kb 5′- GDI2

0.94 (0.91 to 0.98)

0.43

 

*

*

  

[32, 35]

rs16917302

10q21.2

ZNF365 c.981 + 41642A > C

0.75 (0.66 to 0.86)

0.11

B2 + e

 

*

  

[77, 78]

rs10995190

10q21.2

ZNF365 c.981 + 59126G > A

0.76 (0.82 to 0.91)

0.15

A, ER–, B2 + f

*

*

  

[32, 35, 37, 39, 41, 74, 79]

rs704010

10q22.3

ZMIZ1 c.-337 + 12121 T > C

1.07 (1.03 to 1.11)

0.39

A, AA

*

*

  

[32, 35, 37, 41, 58, 80]

rs7904519

10q25.2

TCF7L2 c.382-25857A > G

1.06 (1.02 to 1.10)

0.46

ER–

    

[35, 39]

rs11196174

10q25.2

TCF7L2 c.381 + 22730A > G

1.13 (1.07 to 1.18)

0.31

B1+ only

    

[40]

rs11199914

10q26.12

Intergenic (77 kb 5′-7SK)

0.94 (0.89 to 0.98)

0.32

     

[35]

rs2981582f

10q26.13

FGFR2 c.109 + 906 T > C

1.26 (1.23 to 1.28)

0.39

AA, H, B2+

*

*

*

*

[25, 26, 30, 32, 46, 48, 60, 62]

rs2420946f

10q26.13

FGFR2 c.109 + 1899A > G

1.24 (1.03 to 1.50)

0.38

B2+

    

[26, 41]

rs1219648

10q26.13

FGFR2 c.109 + 7033 T > C

1.23 (1.02 to 1.48)

0.39

AA, A, H

    

[26, 27, 37, 49, 62, 81, 82]

rs2981579

10q26.13

FGFR2 c.110-12117 T > C

1.27 (1.24 to 1.29)

0.40

     

[35]

rs3817198

11p15.5

LSP1 c.*13 + 200 T > C

1.07 (1.04 to 1.11)

0.30

A, B1 + d, B2+

*

*

*

*

[25, 32, 35, 37, 40, 41, 45, 48],[83]

rs909116f

11p15.5

TNNT3 c.-19 + 954 T > C

1.17 (1.10 to 1.24)

0.53

  

*

  

[32]

rs3903072

11q13.1

Intergenic (7.4 kb 3′-CFL1)

0.92 (0.89 to 0.96)

0.47

     

[35]

rs614367

11q13.3

Intergenic

1.15 (1.10 to 1.20)

0.15

A, ER+, B2 + e

*

*

  

[32, 35, 37, 41, 80, 84, 85]

rs11820646

11q24.3

Intergenic (139 kb 3′-BARX2)

0.93 (0.90 to 0.97)

0.41

A, ER–

    

[35, 37, 39]

rs27633

12p11.22

PTHLH c.-266 + 555A > C

1.14 (1.07 to 1.21)

0.39

B2+ only

    

[41]

rs10771399

12p11.22

Intergenic, 29 kb 5′- PTHLH

0.85 (0.83 to 0.88)

0.12

A, B1+, B2 + e, ER–

*

   

[34, 35, 37, 39, 40, 74]

rs12422552

12p13.1

Intergenic (11 kb 5′-U6)

1.11 (1.05 to 1.16)

0.26

A

    

[35, 37]

rs17356907

12q22

Intergenic (16 kb 3′-Y_RNA)

0.89 (0.85 to 0.93)

0.3

A, ER–

    

[35, 37, 39]

rs1292011

12q24.21

Intergenic

0.92 (0.91 to 0.94)

0.41

A, B2 + e

    

[34, 35, 37, 80]

rs11571833

13q13.1

BRCA2 p.Lys3326Ter

1.39 (1.13 to 1.71)

0.01

ER–

    

[35, 39]

rs2236007

14q13.3

PAX9 c.631 + 41G > A

0.88 (0.83 to 0.93)

0.21

A

    

[35, 37]

rs2588809

14q24.1

RAD51B c.757-98173 T > C

1.07 (1.01 to 1.13)

0.16

     

[35]

rs999737

14q24.1

RAD51B c.1037-43041C > T

0.94 (0.88 to 0.99)

0.24

AA, ER–, B1 + d

*

*

*

 

[30, 32, 35, 36, 40, 42, 47, 66],[70]

rs941764

14q32.11

CCDC88C c.271-15014 T > C

1.05 (1.00 to 1.09)

0.34

     

[35]

rs3803662

16q12.1

Intergenic , 5′ to TOX3

1.20 (1.16 to 1.24)

0.25

A, AA, B1 + e, B2+, MBC, ER–

*

*

*

*

[25, 27, 32, 35, 37, 39, 41, 46],[55, 60, 66, 70, 73, 78]

rs4784227

16q12.1

Intergenic, 5' to TOX3

1.27 (1.22 to 1.32)

0.25

A

    

[37]

rs17817449

16q12.2

FTO c.-215-30685 T > G

0.95 (0.91 to 0.99)

0.4

ER–

    

[35, 39]

rs13329835

16q23.2

CDYL2 c.1007 + 3855 T > C

1.14 (1.09 to 1.19)

0.22

AA

    

[35, 42]

rs2075555f

17q21.33

COL1A1 c.804 + 80A > C

No association

0.14

  

*

  

[86]

rs6504950

17q22

STXBP4 c.-156-6504G > A

0.95 (0.92 to 0.97)

0.27

ER–

*

*

  

[31, 39, 41, 87]

rs527616

18q11.2

Intergenic

0.91 (0.87 to 0.95)

0.38

     

[35]

rs1436904

18q11.2

CHST9 c.202 + 33413A > C

0.93 (0.9 to 0.97)

0.4

     

[35]

rs8170 e

19p13.1

BABAM1 c.837G > A

1.26 (1.17 to 1.35)

0.20

AA, B1+, ER–

*

   

[35, 39–42, 58, 66, 77]

rs4808801

19p13.11

ELL c.744 + 1247 T > C

0.94 (0.90 to 0.98)

0.35

AA, ER–

    

[35, 39, 42]

rs1982073f

19q13.2

TGFB1 p.Pro10Leu

1.08 (1.04 to 1.11)

0.38

     

[23, 24, 44]

rs3760982

19q13.31

Intergenic (1.1 kb 5′-KCNN4)

1.06 (1.02 to 1.10)

0.46

     

[35]

rs2284378f

20q11

RALY c.-93 + 6158 T > C

1.08 (1.05 to 1.12)

0.35

     

[63]

rs13039229

20q13.33

Intergenic (2.1 kb 3′ of PTK6)

0.90 (0.84 to 0.97)

0.21

B2+ only

    

[41]

rs311499f

20q13.33

Intergenic (1.4 kb 3′-GMEB2)

0.72 (0.61 to 0.85)

0.07

B2+ only

    

[78]

rs2823093

21q21

Intergenic (5′ to NRIP1 )

0.94 (0.92 to 0.96)

0.27

     

[34, 35]

rs132390

22q12.2

EMID1 c.403 + 272C > T

1.36 (1.19 to 1.54)

0.04

     

[35]

rs6001930

22q13.1

MKL1 c.-59-16944A > G

1.17 (1.11 to 1.25)

0.11

ER–

    

[39]

rs619373

Xq27.1

FGF13 c.50-73946C > T

1.30 (1.17 to 1.45)

0.03

B2+ only

    

[41]

  1. COGS, Collaborative Oncological Gene–environment Study; EA, European descent; ER, estrogen receptor; GWAS, genome-wide association studies; PRS, polygenic risk score; RAF, risk allele frequency; SNP, single nucleotide polymorphism. aBold SNPs are considered the established breast cancer loci pre-COGS. All SNPs listed are in independent linkage disequilibrium blocks as determined using HaploReg with r2 >0.8, with the exception of the 2q33.1 SNPs rs1045485 and rs17468277. Two SNPs in linkage disequilibrium with listed SNP were tested in other populations; that is, rs76972116 at 4q34, and rs7107217 at 11q24. bHuman Genome Variation Society (HGVS) names are given for variants found with the coding region of a gene using the designation for transcript variant #1 as per the Ensembl/UCSC GRCh37/hg19 human genome assembly. cAll SNPs have been identified in populations of European descent (EA) and unselected for ER status; if other populations have been studied, this is noted. If a SNP has been identified only in a subpopulation, it is denoted with 'only’. A, Asian; AA, African-American; AJ, Ashkenazi Jewish; B1+, BRCA1-positive; B2+, BRCA2-positive; H, Hispanic; ER+, estrogen receptor-positive breast cancer; ER–, estrogen receptor-negative breast cancer; MBC, male breast cancer. SNP association listed for population subtype if reported P <10–3.
  2. dPolygenic risk scores are from: model A, Sawyer and colleagues [88]; model B, Husing and colleagues [89]; model C, Wacholder and colleagues [90]; model D, Gail [91]. eSNPs showing borderline association with breast cancer risk in COGS; if population specific, this is indicated in the Additional populations studied column. fSNPs that were not studied in any COGS study [35, 37, 39–42]; if population specific, this is indicated in the Additional populations studied column. gSNPs showing no association with breast cancer risk in COGS; if population specific, this is indicated in the Additional populations studied column.