Table 1 Twenty-seven signals independently associated with systemic sclerosis in the meta-GWAS

From: GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways

Chr

Locus

Bp

SNP

Index SNP

Ref.

MAF

N

P value

OR

Q

I

P cond

Func refgene

1

IL12RB2

67814440

rs3790566

Yes

T

0.24

13

3.84E-10

1.16

0.80

0

-

Intronic

1

CD247

167420425

rs2056626

Yes

G

0.39

6

1.31E-11

0.81

0.57

0

-

Intronic

1

TNFSF4- LOC100506023 -PRDX6

173238736

rs2022449

No

T

0.23

12

6.28E-08

1.15

0.90

0

6.63E-08

Regulatory region

1

TNFSF4- LOC100506023 -PRDX6

173332629

rs1857066

Yes

A

0.25

13

5.02E-09

0.87

0.84

0

-

ncRNA intronic

2

NAB1*

191534372

rs16832798

Yes

C

0.14

14

5.20E-09

1.18

0.41

3.79

3.84E-07

Intronic

2

STAT4

191902758

rs3821236

Yes

A

0.20

12

1.94E-23

1.31

0.03

48.21

-

Intronic

2

STAT4

191959489

rs4853458

No

A

0.23

9

4.86E-18

1.35

0.42

1.79

5.58E-08

Intronic

3

FLNB -DNASE1L3-PXK

58131515

rs7355798

No

T

0.24

13

1.24E-08

1.14

0.14

30.5

7.42E-07

Intronic

3

FLNB-DNASE1L3- PXK

58375286

rs4076852

Yes

G

0.26

13

1.04E-10

1.16

0.71

0

-

Intronic

3

POGLUT1-TIMMDC1-CD80- ARHGAP31

119116150

rs9884090

Yes

A

0.16

13

1.89E-10

0.83

0.92

0

-

Intronic

3

IL12A

159733527

rs589446

Yes

T

0.35

11

1.95E-10

0.86

0.85

0

-

ncRNA intronic

4

DGKQ

965779

rs11724804

Yes

A

0.44

12

5.31E-11

1.17

0.24

21.04

-

Intronic

4

NFKB1

103449041

rs230534

Yes

T

0.34

10

5.38E-09

1.15

0.92

0

-

Intronic

5

TNIP1

150455732

rs3792783

Yes

G

0.16

14

2.42E-12

1.20

0.03

47.41

-

Intronic

6

ATG5

106734040

rs633724

Yes

T

0.35

14

2.84E-09

1.13

0.31

13.41

-

Intronic

7

IRF5- TNPO3

128651522

rs36073657

Yes

T

0.10

12

3.10E-21

1.40

0.21

23.35

-

Intronic

7

IRF5- TNPO3

128658739

rs12155080

No

G

0.37

13

2.87E-13

0.85

0.69

0

2.22E-07

Intronic

8

FAM167A-BLK

11343973

rs2736340

Yes

T

0.24

14

3.33E-21

1.24

0.17

26.76

-

Intergenic

8

RAB2A-CHD7

61564964

rs685985

Yes

T

0.47

11

3.82E-08

0.87

0.15

30.84

-

Intergenic

11

CDHR5 -IRF7

618172

rs6598008

Yes

A

0.44

4

1.97E-08

0.80

0.16

42.27

-

Intronic

11

TSPAN32,CD81-AS1

2348619

rs2651804

Yes

T

0.17

12

2.54E-10

0.82

0.67

0

-

Intergenic

11

DDX6

118639353

rs11217020

Yes

A

0.20

14

2.08E-11

0.84

0.80

0

-

Intronic

15

CSK

75077367

rs1378942

Yes

C

0.39

13

1.84E-14

1.18

0.90

0

-

Intronic

16

IRF8

85971922

rs11117420

Yes

C

0.19

12

3.82E-15

0.81

0.47

0

-

Intergenic

17

IKZF3 -GSDMB

38063381

rs883770

Yes

T

0.50

14

4.79E-09

1.13

0.75

0

-

Intronic

17

NUP85 -GRB2

73224639

rs1005714

Yes

G

0.20

13

1.87E-08

0.85

0.68

0

-

Intronic

19

IL12RB1

18193191

rs2305743

Yes

A

0.20

12

4.64E-10

0.83

0.28

16.88

-

Intronic

  1. The new genome-wide significant loci for systemic sclerosis are highlighted in bold. NAB1-rs16832798 p value conditioned on conditioned on STAT4-rs3821236 and STAT4-rs4853458. For those intronic or regulatory SNPs that are located in a high gene density region, the gene they lie in was underlined
  2. Bp base pair, Chr chromosome, MAF minor allele frequency in the 1000 Genome Project European Population, N number of cohorts, OR odds ratio, Pcond p value conditioned on index SNP, Ref. reference allele, SNP single-nucleotide polymorphism
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