Table 1 Distribution, minor allele frequencies and functional prediction of the selected breast cancer common variants

1q32.1

rs4245739

A/C

C

Intergenic

6

No association

3UTR MDM4 miR-191 target site and results in decreased MDM4 expression

2p24.1

rs12710696

T/C

T

Intergenic

4

No association

TF binding and DNase peak

2q31.1

rs1550623

A/G

G

Intergenic

4

No association

TF binding and DNase peak

4q21

rs1494961

C/T

C

Exonic HELQ c.916G > A

1f

No association

Tolerated

4q21

rs11099601

C/T

C

3 UTR FAM175A c.413 C > T

1f

p = 1.94 × 10⁻²¹ with MRPS18C

DAE eQTL and TF binding / DNase peak

4q34.1

rs6828523

C/A

A

Intronic, ADAM29 c.-450-5711C > A

No data

No association

No data

6p23

rs204247

A/G

G

Intergenic (11 kb 5′-RANBP9)

6

No association

Minimal functional evidence

6q25.1

rs2046210

G/A

A

Intergenic, 6 kb 3’-CCDC170

6

No association

Minimal functional evidence

7q35

rs720475

G/A

A

Intronic; ARHGEF5 c.4531 + 646G > A

5

p = 1.4 × 10⁻⁶ with ARHGEF34P gene and p = 4.2 10^− 6 for OR2A9P gene

TF binding or DNase peak

9q31.2

rs10759243

C/A

A

Intergenic (53 kb 5′-KLF4)

No data

No association

No data

10p12.31

rs7072776

G/A

A

Intergenic (382 bp 3′ MLLT10)

5

No association

TF binding or DNase peak

10p15.1

rs2380205

C/T

T

Intergenic, 2.6 kb 5′-GDI2

3a

No association

TF binding, any motif and DNase peak

10q22.3

rs704010

C/T

T

Intronic; ZMIZ1 c.-337 + 12,121 T > C

2b

No association

TF binding, any motif, DNase Footprint and DNase peak

10q26

rs1219648

A/G

G

Intronic; FGFR2 c.109 + 7033 T > C

No data

No association

No data

10q26

rs2981582

G/A

A

Intronic, FGFR2 c.109 + 906 T > C

5

No association

TF binding or DNase peak

11q13.1

rs3903072

G/T

T

Intergenic (7.4 kb 3′-CFL1)

4

p = 9 × 10⁻⁶ for SNX32, and p = 2.9 × 10^− 5 for CTSW

TF binding and DNase peak

11p15.5

rs3817198

T/C

C

3UTR LSP1 c. 13 + 200 T > C

5

No association

TF binding or DNase peak

12q24.21

rs1292011

A/G

G

Intergenic

4

No association

TF binding and DNase peak

14q24.1

rs2588809

C/T

T

Intronic RAD51B c.757–98,173 T > C

No data

No association

No data

14q32.11

rs941764

A/G

G

Intronic CCDC88C c.271–15,014 T > C

4

No association

TF binding and DNase peak

16q12.1

rs3803662

G/A

A

Intergenic, 5′ to TOX3

5

No association

TF binding or DNase peak

16q12.1

rs8051542

C/T

T

Intronic TOX3 c.88–3168 A > G

5

No association

TF binding or DNase peak

16q23.2

rs13329835

A/G

G

Intronic CDYL2 c.1007 + 3855 T > C

4

No association

TF binding and DNase peak

17q21

rs9911630

A/G

G

3’of BRCA1 NC_000017.10:g.41188342A > G

1b

p = 1.2 × 10⁻²³ for NBR2 and p = 1.3 × 10⁻⁶ for CTD-3199 J23.6 and p = 6.1 × 10⁻⁶ for LINC00854

eQTL, TF binding, any motif, DNase Footprint and DNase peak

17q21

rs799916

T/G

T

Intronic BRCA1 c.4097-141A > C

6

p = 2.1 × 10⁻²⁵ for NBR2 p = 8.3 × 10⁻⁷ for CTD-3199 J23.6 and p = 3.7 × 10⁻⁶ for LINC00854

Minimal functional evidence

18q11.2

rs1436904

T/G

G

Intronic CHST9 c.202 + 33413A > C

No data

No association

No data

19p13.11

rs4808801

A/G

G

Intronic ELL c.744 + 1247 T > C

1f

p = 1.6 × 10⁻⁵ for SSBP4

eQTL, TF binding and/or DNase peak

22q13.1

rs6001930

T/C

C

Intronic MKL1 c.-59-16944A > G

5

No association

TF binding or DNase peak