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Table 2 SNPs with genome-wide significance were namely used as instrumental variables for NAFLD and PCOS in European ancestry individuals

From: The hepato-ovarian axis: genetic evidence for a causal association between non-alcoholic fatty liver disease and polycystic ovary syndrome

Phenotype

SNP

CHR

Position

Gene

EA

OA

EAF

Beta

SE

P value

F statistics

Primary analysis datasets

 NAFLD (Anstee et al. GWAS)

rs2068834a

2

27839539

ZNF512

C

T

0.275

0.264

0.041

8.5×10−11

42.1

rs13118664

4

88239609

HSD17B13

T

A

0.251

−0.302

0.053

1.4×10−08

32.2

rs17216588

19

19664077

CILP2

T

C

0.077

0.477

0.064

7.2×10−14

56.0

rs738409

22

44324727

PNPLA3

G

C

0.224

0.603

0.041

1.5×10−49

219.1

 PCOS (Day et al. GWAS)

rs7563201

2

43561780

THADA

A

G

0.450

−0.108

0.017

3.7×10−10

39.5

rs2178575

2

213391766

ERBB4

A

G

0.150

0.166

0.022

3.3×10−14

57.7

rs13164856

5

131813204

IRF1/RAD50

T

C

0.730

0.124

0.019

1.4×10−10

40.9

rs804279

8

11623889

GATA4/NEIL2

A

T

0.260

0.128

0.018

3.8×10−12

48.1

rs10739076

9

5440589

PLGRKT

A

C

0.310

0.110

0.020

2.5×10−08

31.0

rs7864171

9

97723266

FANCC

A

G

0.430

−0.093

0.017

2.9×10−08

30.8

rs9696009

9

126619233

DENND1A

A

G

0.070

0.202

0.031

8.0×10−11

42.2

rs11031005

11

30226356

ARL14EP/FSHB

T

C

0.850

−0.159

0.022

8.7×10−13

51.0

rs11225154

11

102043240

YAP1

A

G

0.090

0.179

0.027

5.4×10−11

43.2

rs1784692

11

113949232

ZBTB16

T

C

0.820

0.144

0.023

1.9×10−10

40.5

rs2271194

12

56477694

ERBB3/RAB5B

A

T

0.420

0.097

0.017

4.6×10−09

34.2

rs1795379

12

75941042

KRR1

T

C

0.240

−0.117

0.020

1.8×10−09

36.2

rs8043701

16

52375777

TOX3

A

T

0.820

−0.127

0.021

9.6×10−10

37.5

Replication analysis datasets

 NAFLD (UKB GWAS)

rs2807834

1

220970593

MARC1

T

G

0.309

−0.132

0.021

1.1×10−10

41.7

rs1260326

2

27730940

GCKR

T

C

0.388

0.132

0.019

4.0×10−12

48.1

rs17321515

8

126486409

TRIB1

G

A

0.473

−0.145

0.019

1.4×10−14

59.2

rs73001065

19

19460541

MAU2

C

G

0.068

0.327

0.034

1.7×10−22

95.2

rs429358a

19

45411941

APOE

C

T

0.154

−0.202

0.027

5.3×10−14

56.6

rs3747207

22

44324855

PNPLA3

A

G

0.215

0.340

0.022

3.5×10−56

249.4

 PCOS (GWAS meta-analysis of data from FinnGen and EstBB)

rs7564590

2

213387900

ERBB4

T

C

0.356

0.171

0.026

4.8×10−11

43.3

rs9312937

5

16836005

MYO10

T

C

0.554

−0.148

0.026

1.8×10−08

31.8

rs3945628

9

126535553

DENND1A

T

C

0.930

−0.340

0.049

2.9×10−12

48.7

rs11031002

11

30215261

FSHB

A

T

0.122

0.217

0.038

9.3×10−09

32.9

rs1672716

11

113952497

ZBTB16

A

G

0.855

0.206

0.036

9.8×10−09

32.8

rs17880096

22

29105202

CHEK2

C

G

0.037

0.335

0.047

1.5×10−12

50.0

  1. Genomic positions reported in the GWASs refer to human reference assembly (GRCh37/hg19)
  2. Abbreviations: CHR chromosome, EA effect allele, EAF effect allele frequency, EstBB Estonian Biobank, NAFLD non-alcoholic fatty liver disease, OA other alleles (reference allele), PCOS polycystic ovary syndrome, SE standard error, SNP single nucleotide polymorphism
  3. ars2068834 and rs429358 were excluded from the sensitivity analysis due to their genome-wide significant association with obesity
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BMC Medicine

ISSN: 1741-7015

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