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Table 1 Lead SNPs of the genome-wide significant loci identified in the GWAS meta-analysis of mammographic dense area (DA), non-dense area (NDA) and percent mammographic density (PMD)

From: Genome-wide and transcriptome-wide association studies of mammographic density phenotypes reveal novel loci

Region

rs ID

Chromosome

Position1

Gene2

Alleles3

MAF4

Z-score5

p Value

Novel locus6

DA (N = 18)

1q21.2

rs11205303

1

149,906,413

MTMR11

T/C

0.369

 − 6.772

1.25E−11

No

2q14.2

rs17625845

2

121,089,731

INHBB

T/C

0.221

7.949

1.87 E−15

No

4q13.3

rs6851733

4

75,518,708

AREG

T/C

0.226

6.874

6.23 E−12

No

5q11.2

rs150249911

5

52,119,132

ITGA1

A/G

0.018

 − 5.928

3.06 E−09

Yes

5q23.2

rs335189

5

122,446,856

PRDM6

C/G

0.265

6.655

2.84 E−11

No

5q35.1

rs2042239

5

169,566,329

DOCK2

A/G

0.354

6.485

8.87 E−09

Yes

6q25.1

rs9397436

6

151,952,002

ESR1

A/G

0.073

7.951

1.86 E−15

No

7p11.2

rs10155920

7

55,308,930

ELDR

T/C

0.145

5.755

8.66 E−09

Yes

8q24.13

rs58847541

8

124,610,166

–

A/G

0.153

5.994

2.05 E−09

Yes

10q21.2

rs10995187

10

64,273,026

ZNF365

A/G

0.148

8.933

4.14 E−19

No

11p15.5

rs4980383

11

1,902,097

LSP1

T/C

0.451

 − 7.228

4.90 E−13

No

12p12.1

rs11836164

12

26,446,625

SSPN/ITPR2

T/C

0.248

6.028

1.66 E−09

No

12p11.2

rs7297051

12

28,174,817

PTHLH

T/C

0.233

6.166

7.01 E−10

Yes

12q23.2

rs833472

12

103,005,100

IGF1

T/C

0.032

7.134

9.76 E−13

No

19q13.33

rs1231281

19

49,239,200

FUT2/MAMSTR

A/G

0.458

6.860

6.87 E−12

No

20q13.13

rs17789629

20

48,892,374

SMIM25

A/C

0.137

 − 5.478

4.30 E−08

No

22q13.1

rs34066050

22

38,612,604

TMEM184B

A/G

0.467

 − 5.534

3.14 E−08

No

22q13.2

rs6001939

22

40,892,794

MKL1

T/C

0.102

8.791

1.48 E−18

No

NDA (N = 6)

1p12

rs78395856

1

119,495,096

TBX15

A/C

0.046

5.525

3.29 E−08

No

5q14.1

rs413472

5

80,930,992

SSBP2

T/C

0.445

5.551

2.84 E−08

Yes

8p11.23

rs16885613

8

36,848,357

–

T/C

0.148

 − 12.788

1.92 E−37

No

10q21.2

rs2138555

10

64,220,494

ZNF365

A/G

0.419

5.900

3.63 E−09

No

12q22

rs61938093

12

96,026,737

NTN4

T/C

0.290

 − 6.266

3.72 E−10

No

22q13.2

rs73169097

22

41,027,870

MKL1

T/C

0.100

6.012

1.83 E−09

No

PMD (N = 15)

1q21.2

rs1868992

1

149,908,108

MTMR11

A/G

0.259

5.517

3.44 E−08

No

5q23.2

rs335189

5

122,446,856

PRDM6

C/G

0.265

6.196

5.78 E−10

No

5q31.1

rs76876329

5

131,237,759

MEIKIN

T/C

0.151

5.530

3.21 E−08

Yes

5q33.3

rs11745230

5

158,171,008

EBF1

T/G

0.166

 − 5.793

6.90 E−09

Yes

5q35.1

rs2112670

5

169,557,594

DOCK2

A/G

0.345

 − 5.598

2.17 E−08

Yes

6p22.3

rs3819405

6

16,399,557

ATXN1

T/C

0.340

5.806

6.42 E−09

No

6q25.1

rs4897107

6

149,601,591

TAB2

T/C

0.162

6.842

7.81 E−12

No

6q25.1

rs9397436

6

151,952,002

ESR1

A/G

0.073

7.303

2.81 E−13

No

8p11.23

rs10087804

8

36,858,140

–

C/G

0.142

6.282

3.35 E−10

No

10q21.2

rs10995187

10

64,273,026

ZNF365

A/G

0.148

10.424

1.92 E−25

No

11p15.5

rs4980383

11

1,902,097

LSP1

T/C

0.451

 − 5.860

4.62 E−09

No

12q23.2

rs61941038

12

102,989,316

IGF1

A/T

0.033

 − 6.477

9.37 E−11

No

15q26.1

rs4499190

15

94,275,057

–

G/C

0.341

 − 5.654

1.57 E−08

No

16q12.2

rs11646715

16

53,824,007

FTO

A/G

0.456

7.183

6.84 E−13

Yes

19q13.33

rs12462111

19

49,171,306

FUT2/MAMSTR

T/C

0.427

5.847

5.02 E−09

No

  1. 1Genomic positions based on build GRCh37/hg19
  2. 2Closest gene to the lead variant
  3. 3Coded as reference allele/effect allele
  4. 4Minor allele frequency, based on the European Ancestry population in the 1000 Genome project
  5. 5Z-scores were obtained using sample size weighted meta-analysis of GWAS. The multivariate linear regression model used in GWAS analysis adjusted for age and BMI at mammogram, as well as the first ten principal components representing population structure. Additive inheritance model was used. Square-root transformed mammographic density phenotypes were used as the outcome variable
  6. 6Whether the locus is novel (Yes) or has previously been reported (No) to be associated with at least one MD phenotype in the literature
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Breast Cancer Research

ISSN: 1465-542X

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