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Table 3 Major SNP association results with NAFLD (case-control), and 4 quantitative case-only GWA studies (NAS score, fibrosis, liver enzymes ALT and AST) in the eMERGE Network. All results adjusted for age, gender, site of genotyping, 3 first principal components, and BMI. For more details and results with p < 10− 5, see Additional file 1: Table S2

From: GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network

NAFLD-GWAS

 SNP

CHR

Positiona

Gene

Minor allele

MAFb

OR

L95

U95

p

 rs738409

22

44,324,727

PNPLA3

G

0.23

1.79

1.58

2.02

1.70 × 10−20

 rs738408

22

44,324,730

PNPLA3

T

0.23

1.79

1.58

2.02

1.93 × 10−20

 rs3747207

22

44,324,855

PNPLA3

A

0.23

1.78

1.58

2.02

2.63 × 10−20

 rs2294915

22

44,340,904

PNPLA3

T

0.25

1.75

1.55

1.97

1.40 × 10−19

 rs2980888

8

126,507,308

TRIB1

T

0.31

1.36

1.20

1.53

5.98 × 10−07

 rs2954038

8

126,507,389

TRIB1

C

0.31

1.35

1.20

1.52

8.30 × 10−07

NAS score

 

 SNP

CHR

Position

Gene

Minor allele

MAF

Beta

SE

p

 

 rs5748926

22

17,649,774

IL17RA

T

0.34

0.91

0.16

3.81 × 10−08

 

 rs738409

22

44,324,727

PNPLA3

G

0.41

0.85

0.15

3.94 × 10−08

 

Fibrosis

 

 SNP

CHR

Position

Gene

Minor allele

MAF

Beta

SE

p

 

 rs698718

16

68,560,185

ZFP90-CDH1

A

0.23

0.83

0.12

2.74 × 10−11

 

 rs1645976

16

68,563,509

ZFP90-CDH1

T

0.23

0.83

0.12

2.79 × 10−11

 

 rs72943235

2

88,500,646

FABP1

A

0.01

2.38

0.43

8.18 × 10−08

 

ALT liver enzyme

 

 SNP

CHR

Position

Gene

Minor allele

MAF

Beta

SE

p

 

 rs206833

2

31,708,616

XDH

A

0.17

0.26

0.05

3.41 × 10−07

 

 rs2294915

22

44,340,904

PNPLA3

T

0.34

0.20

0.04

4.04 × 10−07

 

 rs738409

22

44,324,727

PNPLA3

G

0.33

0.20

0.04

4.68 × 10−07

 

AST liver enzyme

 

 SNP

CHR

Position

Gene

Minor allele

MAF

Beta

SE

p

 

 rs10272006

7

21,520,132

SP4

G

0.33

0.25

0.04

5.83 × 10−09

 

 rs7796796

7

21,499,857

SP4

A

0.32

0.25

0.04

6.29 × 10− 09

 

 rs62141163

2

31,663,114

XDH

A

0.11

0.34

0.07

2.30 × 10−07

 
  1. Abbreviations: MAF minor allele frequency, OR odds ratio, and 95% confidence interval (CI), Beta change in quantitative case-only phenotypes (NAS score, fibrosis (235 cases), ALT and AST liver enzymes (1075 cases)) per copy of minor allele (direction of beta is for minor alleles, SE standard error of beta; aPosition = GRch37/hg19; bThe direction of all effects is for the minor allele. The minor allele frequency for case-only GWA results is for cases