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Table 2 26 pleiotropic genomic loci identified by FUMA using PLACO results

From: The shared genetic landscape of polycystic ovary syndrome and breast cancer: convergence on ER + breast cancer but not ER- breast cancer

Trait pair

Top SNP

Locus boundary

Region

Nearest gene

PP.H3

PP.H4

Best causal SNP

SNP.PP.H4

PCOS-BCALL

rs10423928

19:46,179,043–46202172

19q13.32

GIPR

2.53E-01

2.28E-02

rs4849879

1.40E-01

PCOS-BCALL

rs11012730

10:21,766,969–22,275,118

10p12.31

SKIDA1

1.99E-01

1.63E-02

rs552647

1.24E-01

PCOS-BCALL

rs147872430

5:44,992,980–45933347

5p12

NA

4.53E-02

2.14E-02

rs930395

7.44E-01

PCOS-BCALL

rs17630711

3:27,421,024–27553889

3p24.1

SLC4A7

2.91E-01

2.43E-02

rs60954078

2.13E-01

PCOS-BCALL

rs2926589

8:76,362,101–76689287

8q21.13

HNF4G

1.93E-01

5.37E-02

rs72658071

4.03E-01

PCOS-BCALL

rs45577136

16:52,566,220–52630972

16q12.1

TOX3

8.82E-02

1.22E-01

rs12251016

2.07E-01

PCOS-BCALL

rs4980554

11:69,281,227–69,285,786

11q13.3

NA

2.00E-01

1.35E-02

rs719338

2.76E-01

PCOS-BCALL

rs61874140

10:123,435,982–123,435,982

10q26.13

NA

1.33E-01

1.31E-02

rs2981579

8.35E-01

PCOS-BCALL

rs73949122

2:121,153,284–121,180,803

2q14.2

NA

1.39E-01

2.37E-02

rs78540526

1.00E + 00

PCOS-BCALL

rs753271

10:80,853,575–80869471

10q22.3

ZMIZ1

2.41E-01

1.97E-02

rs4784227

9.55E-01

PCOS-BCALL

rs8050136

16:53,797,908–53845487

16q12.2

FTO

1.83E-01

8.12E-01

rs62048402

2.03E-01

PCOS-BCALL

rs851984

6:151,970,639–152052215

6q25.1

ESR1

7.87E-02

6.43E-01

rs10423928

2.69E-01

PCOS-ERNBC

rs1121980

16:53,797,908–53845487

16q12.2

FTO

2.37E-01

7.79E-02

rs4528762

9.99E-01

PCOS-ERNBC

rs1293960

6:151,970,639–151970639

6q25.1

NA

2.83E-01

2.43E-02

rs9397437

2.28E-01

PCOS-ERNBC

rs4849857

2:120,986,708–121070811

2q14.2

NA

1.60E-01

8.35E-01

rs55872725

9.14E-02

PCOS-ERPBC

rs10423928

19:46,179,043–46202172

19q13.32

GIPR

1.66E-01

1.70E-02

rs490706

6.21E-02

PCOS-ERPBC

rs11012730

10:21,766,969–22,275,118

10p12.31

SKIDA1

1.42E-01

3.64E-02

rs985261

3.97E-02

PCOS-ERPBC

rs11706019

3:27,421,024–27553889

3p24.1

SLC4A7

2.91E-01

2.43E-02

rs60954078

3.34E-01

PCOS-ERPBC

rs12380632

9:110,891,494–110941095

9q31.2

LOC105376214

1.30E-01

1.41E-02

rs7862747

2.54E-01

PCOS-ERPBC

rs13131992

4:175,819,086–175870676

4q34.1

ADAM29

8.71E-02

1.32E-01

rs10828248

2.73E-01

PCOS-ERPBC

rs45577136

16:52,566,220–52630972

16q12.1

TOX3

1.33E-01

1.31E-02

rs2981579

7.34E-01

PCOS-ERPBC

rs4980554

11:69,281,227–69,285,786

11q13.3

NA

1.39E-01

2.37E-02

rs78540526

1.00E + 00

PCOS-ERPBC

rs61874140

10:123,435,982–123,435,982

10q26.13

NA

2.41E-01

1.94E-02

rs4784227

9.93E-01

PCOS-ERPBC

rs715537

22:28,625,685–29,257,046

22q12.1

NA

1.45E-01

8.50E-01

rs62048402

1.29E-01

PCOS-ERPBC

rs8050136

16:53,797,908–53845487

16q12.2

FTO

1.05E-01

5.24E-01

rs10423928

3.40E-01

PCOS-ERPBC

rs851984

6:152,008,780–152024985

6q25.1

ESR1

1.84E-01

4.62E-02

rs62237573

1.00E + 00

  1. PCOS, polycystic ovary syndrome; BC, breast cancer; ERNBC, estrogen receptor-negative breast cancer; ERPBC, estrogen receptor-positive breast cancer; Best causal, the candidate causal single-nucleotide polymorphism (SNP); PP.H3, posterior probability of H3; PP.H4, posterior probability of H4; SNP.PP.H4, posterior probability of the best causal polymorphism. Locus boundary of each pleiotropic genomic risk locus was denoted as “chromosome: start–end” defined by FUMA for the corresponding trait pair. The top SNP in this locus was also identified as a candidate causal SNP
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Breast Cancer Research

ISSN: 1465-542X

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