Table 1 Summary results of the GWAS and meta-analysis of Sjögren’s of European Ancestry.

From: Genome-wide association study identifies Sjögren’s risk loci with functional implications in immune and glandular cells

Index gene

Other disease associationsa

GWAS

Immunochip

Meta

SNP rsID

Chr

Base pair

minb

mafc

MAFd

O/Ie

OR (95%CI)

P value

O/I

OR (95%CI)

P value

P value

Novel significant loci by GWAS (P < 5 × 10−8):

NAB1

 

IIM, MS, PBC, RA, SLE, SSc

          

rs2293765

2

191520845

C

A

0.41

O

1.24 (1.17–1.32)

5.53 × 10−14

–

–

–

–

rs11900804

2

191533767

C

T

0.42

I

1.22 (1.16–1.30)

2.44 × 10−12

–

–

–

–

rs2192008

2

191545147

A

G

0.42

I

1.23 (1.16–1.30)

1.37 × 10−12

I

1.22 (1.07–1.40)

2.71 × 10−03

2.18 × 10−14

rs744600

2

191564757

G

T

0.38

I

1.22 (1.16–1.30)

2.89 × 10−12

I

1.27 (1.11–1.45)

4.53 × 10−03

6.07 × 10−15

rs10202868

2

191563991

C

T

0.25

I

0.88 (0.83–0.95)

5.49 × 10−4

O

0.89 (0.76–1.04)

0.16

2.24 × 10−4

PTTG1-MIR146A

 

SLE

          

rs2910194

5

159844175

T

C

0.49

I

1.11 (1.05–1.18)

1.53 × 10−04

O

1.11 (0.97–1.27)

0.06

4.34 × 10-05

rs2431698

5

159884083

T

G

0.47

I

0.84 (0.81–0.89)

2.65 × 10−08

I

0.91 (0.80–1.05)

0.21

5.19 × 10−08

rs2431697

5

159879978

C

T

0.42

O

0.83 (0.79–0.88)

3.33 × 10−09

I

0.91 (0.79–1.04)

0.17

6.61 × 10−09

rs2431099

5

159886620

A

G

0.47

I

0.84 (0.80–0.89)

2.36 × 10−08

O

0.91 (0.80–1.05)

0.21

4.79 × 10−08

XKR6

 

Asthma, SLE

          

rs4841466

8

10828909

T

C

0.46

I

1.17 (1.11–1.24)

3.77 × 10−08

I

1.40 (1.23–1.60)

3.46 × 10−07

2.73 × 10−13

rs11250098

8

10818607

A

G

0.48

I

1.16 (1.09–1.23)

3.87 × 10−07

I

1.39 (1.22–1.58)

7.77 × 10−07

6.89 × 10−12

rs11250099

8

10818657

A

G

0.47

I

1.17 (1.10–1.24)

5.99 × 10−08

I

1.40 (1.22–1.60)

4.97 × 10−07

5.97 × 10−13

rs4841465

8

10819854

C

T

0.48

O

1.17 (1.10–1.23)

9.42 × 10−08

I

1.42 (1.24–1.62)

1.72 × 10−07

4.85 × 10−13

rs3885690

8

10826869

C

T

0.37

I

0.85 (0.80–0.91)

5.47 × 10−07

O

0.78 (0.68–0.89)

5.45 × 10−04

1.32 × 10−09

MAPT-CRHR1

 

PBC

          

rs7210219

17

44018519

C

T

0.19

I

0.78 (0.72–0.84)

2.40 × 10−10

–

–

–

–

rs2696609

17

44293205

G

A

0.20

I

0.78 (0.72–0.84)

2.77 × 10−10

–

–

–

–

rs7215239

17

43767773

C

T

0.21

O

0.80 (0.75–0.86)

8.74 × 10−09

–

–

–

–

RPTOR-CHMP6-BAIAP6

rs8071514

17

78964083

C

A

0.44

I

0.84 (0.79–0.89)

1.64 × 10−08

–

–

–

–

rs6565516

17

78965146

A

G

0.41

I

0.85 (0.80–0.90)

1.26 × 10−07

–

–

–

–

rs4969331

17

78966915

C

T

0.41

O

0.85 (0.80–0.90)

2.13 × 10−07

–

–

–

–

TYK2

 

ATD, IIM, MS, PBC, RA, SLE, SSc, T1DM

          

rs11085725

19

10462513

T

C

0.28

I

0.78 (0.73–0.83)

7.17 × 10−13

I

0.96 (0.82–1.11)

0.59

8.56 × 10−11

rs74908652

19

10828909

C

T

0.16

I

0.92 (0.85–0.99)

4.54 × 10−02

O

0.79 (0.65–0.95)

1.67 × 10−02

3.43 × 10−03

rs753859

19

10531224

C

G

0.48

I

0.87 (0.82–0.92)

2.56 × 10−06

I

0.92 (0.81–1.05)

0.22

2.88 × 10−06

rs34953890

19

10526854

A

C

0.20

I

0.83 (0.77–0.89)

1.94 × 10−06

I

0.98 (0.83–1.16)

0.84

2.39 × 10−05

rs2304256

19

10475652

A

C

0.28

O

0.79 (0.74–0.84)

9.14 × 10−12

I

0.95 (0.82–1.11)

0.55

5.38 × 10−10

SYNGR1

 

PBC, RA, SLE

          

rs2069235

22

39747780

A

G

0.31

I

1.21 (1.14–1.28)

5.06 × 10−10

–

–

–

–

rs909685

22

39747671

A

T

0.31

I

1.21 (1.14–1.28)

5.90 × 10−10

–

–

–

–

rs3747177

22

39747780

A

C

0.24

I

1.21 (1.14–1.30)

3.93 × 10−09

–

–

–

–

rs5757611

22

39708357

T

C

0.22

O

1.19 (1.11–1.27)

1.70 × 10−07

–

–

–

–

Novel significant loci by meta-analysis (P < 5 × 10−8):

CD247

 

Asthma, ATD, RA, SLE, SSc

          

rs7523907

1

167427247

C

T

0.42

I

0.85 (0.80–0.90)

2.35 × 10−07

I

0.83 (0.73–0.96)

1.14 × 10−02

9.33 × 10−09

rs2949661

1

167424924

T

C

0.37

I

0.86 (0.81–0.91)

2.20 × 10−06

I

0.84 (0.73–0.96)

1.41 × 10−02

9.99 × 10−08

rs1723018

1

167433420

C

T

0.38

I

0.86 (0.81–0.91)

8.08 × 10−07

I

0.83 (0.73–0.92)

1.20 × 10−02

3.22 × 10−08

rs2056626

1

167420425

G

T

0.39

I

0.86 (0.81–0.91)

1.65 × 10−06

O

0.83 (0.73–0.96)

1.10 × 10−02

5.94 × 10−08

rs864537

1

167411384

G

A

0.39

O

0.92 (0.87–0.97)

7.80 × 10−03

O

0.82 (0.71–0.94)

6.49 × 10−03

2.51 × 10−04

PRDM1-ATG5

 

Asthma, RA, SLE SSc

          

rs526531

6

106570056

A

G

0.32

I

1.13 (1.07–1.21)

2.1 × 10−05

O

1.28 (1.11–1.47)

3.84 × 10−04

4.86 × 10−08

rs533733

6

106564236

A

G

0.33

I

1.14 (1.07–1.21)

1.79 × 10−05

I

1.21 (1.05–1.39)

5.27 × 10−03

3.25 × 10−07

rs7768653

6

106574794

T

C

0.41

I

1.13 (1.06–1.19)

3.52 × 10−05

I

1.14 (0.99–1.30)

5.40 × 10−02

5.49 × 10−06

rs4946728

6

106590363

A

C

0.25

O

1.09 (1.02–1.16)

5.13 × 10−03

I

1.15 (0.99–1.33)

5.91 × 10−02

7.62 × 10−04

TNFAIP3

 

RA, SLE, SSc

          

rs61117627

6

138243700

A

G

0.03

I

1.45 (1.26–1.67)

2.52 × 10−07

O

1.42 (1.02–1.98)

3.48 × 10−02

3.32 × 10−08

rs58905141

6

138132123

G

A

0.03

I

1.44 (1.24–1.67)

6.85 × 10−07

I

1.35 (0.96–1.92)

7.81 × 10−02

2.16 × 10−07

rs5029937

6

138195151

T

G

0.03

I

1.43 (1.25–1.65)

3.33 × 10−07

I

1.26 (0.91–1.75)

1.59 × 10−01

2.93 × 10−07

rs5029924

6

138187498

T

C

0.03

I

1.42 (1.23–1.63)

7.75 × 10−07

I

1.28 (0.92–1.77)

1.29 × 10−01

4.62 × 10−07

rs2230926

6

138196066

G

T

0.03

O

1.43 (1.25–1.65)

3.33 × 10−07

I

1.26 (0.91–1.75)

1.59 × 10−01

2.93 × 10−07

rs7749323

6

138230389

A

G

0.03

I

1.43 (1.23–1.65)

1.14 × 10−06

O

1.30 (0.92–1.84)

1.25 × 10−01

6.18 × 10−07

  1. ATD autoimmune thyroid disease, IIM idiopathic inflammatory myopathies, MS multiple sclerosis, PBC primary biliary cirrhosis, RA rheumatoid arthritis, SLE systemic lupus erythematosus, SSc systemic sclerosis, T1DM type 1 diabetes mellitus.
  2. aDisease associations indicated based on NHGRI-EBI GWAS Catalog.
  3. bMinor allele (min); cmajor allele (max); dminor allele frequency (MAF); eobserved (O) or imputed (I) SNP in GWAS or immunochip analyses.
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