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Table 2 SLE risk SNPs association with clinical phenotypes

From: Genome-wide pathway analysis identifies VEGF pathway association with oral ulceration in systemic lupus erythematosus

SNP

Chr

Pos

Gene

RA

Phenotype

P D

P V

P C

OR (CI, 95%)

rs2476601 a

1

114377568

PTPN22

A

Hematologic disorder

0.0039

0.0433

5.20e-4

9.488 (1.310-68.726)

     

Antinuclear antibodies

0.0146

0.0281

0.0011

0.168 (0.004-0.990)

rs704840

1

173226195

TNFSF4

G

Renal disorder

0.0407

0.9210

0.1290

1.199 (0.941-1.527)

rs3024505

1

206939904

IL10

T

Arthritis

0.0325

0.1540

0.0170

1.557 (1.091-2.221)

rs3768792

2

213871709

IKZF2

C

Photosensitivity

0.0437

0.3320

0.4580

0.893 (0.674-1.184)

     

Hematologic disorder

0.0319

0.1880

0.0143

0.507 (0.301-0.855)

rs9311676

3

58470351

ABHD6,PXK

C

Oral ulcers

0.0338

0.7960

0.9210

0.832 (0.674-1.028)

rs564799

3

159728987

IL12A

C

Discoid rash

0.0411

0.1410

0.6853

0.942 (0.674-1.316)

rs1270942

6

31918860

MHC class III

C

Arthritis

0.0138

0.6670

0.0407

1.530 (1.010-2.346)

rs9462027

6

34797241

UHRF1BP1

A

Malar rash

0.0263

0.1730

0.0137

1.333 (1.071-1.660)

     

Oral ulcers

0.0251

0.8950

0.0933

1.210 (0.971-1.508)

rs6932056

6

138242437

TNFAIP3

C

Serositis

0.0193

0.8140

0.1364

1.580 (0.898-2.781)

rs4917014

7

50305863

IKZF1

T

Oral ulcers

0.0280

0.1550

0.5821

0.944 (0.753-1.184)

rs2663052

10

50069395

WDFY4

C

Neurologic disorder

0.0370

0.1590

0.6311

0.963 (0.662-1.401)

rs4948496

10

63805617

ARID5B

C

Malar rash

0.0331

0.4580

0.3258

1.116 (0.906-1.375)

     

Photosensitivity

0.0202

0.9480

0.0911

1.203 (0.977-1.483)

rs2732549

11

35088399

CD44

T

Immunologic disorder

0.0163

0.9910

0.0907

1.277 (0.976-1.670)

rs7941765

11

128499000

ETS1,FLI1

C

Arthritis

0.0072

0.0701

0.0015

1.470 (1.151-1.877)

rs10774625

12

111910219

SH2B3

A

Serositis

0.0207

0.0756

0.0038

0.715 (0.571-0.895)

     

Renal disorder

0.0423

0.6410

0.0773

0.814 (0.650-1.018)

     

Immunologic disorder

0.0051

0.8190

0.0321

0.738 (0.566-0.964)

rs1059312

12

129278864

SLC15A4

C

Serositis

0.0253

0.2370

0.0156

1.321 (1.053-1.658)

rs4902562

14

68731458

RAD51B

A

Renal disorder

0.0130

0.8670

0.1010

0.834 (0.664-1.047)

rs2941509

17

37921194

IKZF3

A

Antinuclear Antibodies

0.0304

0.0413

0.4943

0.676 (0.237-1.930)

rs2304256

19

10475652

TYK2

C

Arthritis

0.0298

0.7690

0.1841

0.826 (0.622-1.096)

  1. A total of 19 SLE risk genetic variants were significantly associated with different systemic lupus erythematosus (SLE) phenotypes in the discovery stage. From these, the association between PTPN22 and hematologic disorder and between PTPN22 and the production of antinuclear antibodies (a) were significantly replicated in the validation cohort. Combining the statistical evidence from the two cohorts, seven additional genetic variants were found to be nominally associated with SLE phenotypes (shown in bold). Abbreviations: SNP single-nucleotide polymorphism, Chr chromosome, Pos SNP base pair in build GRCh37/hg19, RA disease risk allele, P D P value discovery cohort, P V P value validation cohort, P C P value combined, OR odds ratio according to the allele associated with disease risk, CI confidence interval (95%)