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Table 1 Meta-analysis of 66 GWAS-genotyped SNPs in scleroderma (SSc) patients and healthy controls of Caucasian origin

From: A genome-wide association study follow-up suggests a possible role for PPARG in systemic sclerosis susceptibility

Chr

Locus

SNP

Minor/major

MAF cases

MAF controls

P MH

OR (CI 95%)a

P BD

3

PPARG

rs310746

C/T

0.108

0.086

1.90E-06

1.28 [1.12-1.47]

0.33

4

CHRNA9 | RHOH

rs6832151

G/T

0.315

0.281

4.30E-06

1.17 [1.075-1.27]

0.05

2

DYSF

rs11692280

A/G

0.195

0.220

2.31E-04

0.86 [0.80-0.93]

0.04

4

PGDS

rs17021463

T/G

0.393

0.421

2.45E-04

0.89 [0.83-0.94]

0.13

22

DGCR6

rs2543958

G/T

0.127

0.109

4.98E-04

1.18 [1.09-1.28]

0.09

17

ORMDL3/GSDML

rs8079416

C/T

0.435

0.461

1.13E-03

0.90 [0.85-0.94]

0.01

1

-

rs6679637

A/G

0.100

0.116

2.35E-03

0.85 [0.77-0.94]

0.03

1

CSFR3

rs4653210

G/T

0.111

0.122

3.71E-03

0.86 [0.78-0.95]

0.02

3

PPARG/ TSEN2

rs9855622

T/C

0.124

0.110

4.75E-03

1.14 [1.01-1.30]

2.94E-03

7

CACNA2D1

rs1544461

A/G

0.429

0.409

5.14E-03

1.09 [1.02-1.16]

7.81E-04

18

CNDP2

rs2241508

G/A

0.421

0.401

5.26E-03

1.09 [1.03-1.15]

2.94E-04

11

PHF21A/CREB3L1

rs7128538

A/G

0.491

0.470

5.51E-03

1.09 [1.02-1.16]

4.62E-03

14

NPAS3

rs1299512

G/A

0.228

0.211

7.76E-03

1.10 [1.00-1.21]

0.05

13

RFC3

rs7335534

G/A

0.398

0.415

8.61E-03

0.91 [0.84-0.99]

7.34E-04

8

DDEF1

rs7817803

A/C

0.437

0.421

0.012

1.08 [1.01-1.15]

2.01E-03

8

DDE/

rs3057

C/T

0.439

0.423

0.012

1.08 [1.01-1.15]

1.13E-03

17

TMEM132E/CCDC16

rs887081

T/G

0.115

0.129

0.013

0.88 [0.810.95]

5.33E-03

5

CDH18

rs1911856

T/C

0.059

0.048

0.013

1.18 [1.03-1.35]

3.24E-03

7

CAV1

rs2402091

A/G

0.110

0.122

0.014

0.88 [0.80-0.97]

0.02

7

-

rs1228966

A/G

0.222

0.208

0.015

1.09 [1.01-1.18]

2.29E-03

7

SEMA3A

rs1228870

T/G

0.222

0.208

0.017

1.09 [1.01-1.18]

3.15E-03

5

LOC389293

rs7708428

G/A

0.401

0.418

0.019

0.92 [0.87-0.98]

0.01

9

XPA

rs2808699

A/C

0.403

0.423

0.021

0.92 [0.87-0.98]

2.38E-04

8

DDEF1

rs7839523

G/T

0.440

0.425

0.021

1.07 [1.011-1.14]

1.10E-03

9

XPA

rs2805790

A/G

0.403

0.422

0.022

0.92 [0.87-0.98]

3.37E-04

3

IRAK2

rs11706450

T/C

0.465

0.482

0.024

0.93 [0.86-1.01]

9.00E-03

9

XPA

rs2805815

A/G

0.403

0.422

0.024

0.93 [0.87-0.99]

3.02E-04

2

NOL10

rs4668690

A/G

0.067

0.059

0.026

1.15 [1.01-1.30

3.10E-03

7

-

rs1029541

T/C

0.230

0.219

0.028

1.08 [1.01-1.17]

8.07E-04

9

XPA

rs2668797

A/G

0.071

0.112

0.029

0.933 [0.87-0.99]

2.48E-04

14

-

rs1036570

A/G

0.322

0.335

0.032

0.92 [0.85-1.014]

2.13E-03

3

-

rs4128236

T/C

0.322

0.306

0.034

1.07 [0.98-1.17]

3.87E-04

1

-

rs10925871

A/G

0.193

0.181

0.038

1.08 [1.00-1.17]

6.22E-03

7

CADPS2

rs2501439

G/A

0.418

0.432

0.042

0.93 [0.87-0.99]

7.49E-03

7

-

rs757747

T/C

0.229

0.218

0.047

1.07 [1.00-1.16]

1.29E-03

7

WBSCR17

rs4585627

T/C

0.323

0.308

0.051

1.07 [1.00-1.14]

4.70E-03

10

-

rs1254860

C/T

0.110

0.100

0.064

1.09 [0.99-1.21]

0.03

8

DDEF1

rs6470805

G/A

0.333

0.344

0.069

0.94 [0.88-1.00]

4.88E-03

9

LCN9

rs541131

G/A

0.400

0.385

0.071

1.06 [0.99-1.12]

1.78E-03

5

CDH18

rs2202798

T/C

0.080

0.069

0.078

1.11 [0.98-1.24]

9.17E-04

3

TDGF1

rs6799581

G/T

0.260

0.268

0.080

0.94 [0.86-1.03]

6.85E-04

5

CDH18

rs12655266

A/G

0.074

0.065

0.111

1.10 [0.98-1.24]

1.09E-03

4

NPY2R

rs2880417

G/A

0.292

0.281

0.117

1.05 [0.99-1.13]

2.07E-05

7

-

rs10272701

T/C

0.192

0.183

0.130

1.06 [0.98-1.15]

7.73E-03

8

FBX032

rs3739284

C/T

0.219

0.224

0.148

0.94 [0.87-1.01]

3.71E-03

6

ASCC3

rs7771570

C/T

0.492

0.482

0.153

1.04 [0.98-1.11]

2.97E-04

18

PHLPP

rs2877745

T/C

0.091

0.084

0.158

1.08 [0.98-1.18]

3.49E-03

21

-

rs2831511

T/C

0.393

0.403

0.175

0.95 [0.90-1.01]

1.54E-04

11

OPCML

rs10894623

T/G

0.291

0.281

0.175

1.04 [0.95-1.14]

8.98E-04

6

ASCC3

rs6919745

T/C

0.476

0.467

0.190

1.042 [0.98-1.11]

1.88E-04

4

NPY2R

rs13138293

G/T

0.308

0.299

0.195

1.05 [0.97-1.11]

8.20E-05

15

SMAD3

rs4147358

A/C

0.237

0.243

0.203

0.95 [0.86-1.04]

4.76E-04

17

TMEM132E

rs4795032

T/C

0.351

0.341

0.232

1.04 [0.95-1.13]

6.65E-04

9

-

rs10756265

A/G

0.342

0.352

0.251

0.96 [0.90-1.02]

2.18E-04

9

-

rs443042

G/A

0.366

0.376

0.261

0.96 [0.90-1.02]

2.01E-04

9

SUSD3

rs9696357

T/C

0.154

0.160

0.268

0.95 [0.87-1.03]

2.11E-03

12

SFRS8

rs10794423

C/T

0.439

0.442

0.282

0.96 [0.89-1.04]

1.22E-03

2

ATP6V1C2

rs7422405

A/G

0.428

0.433

0.385

0.97 [0.91-1.03]

1.93E-04

3

RBMS3

rs35883

A/G

0.457

0.4564

0.556

1.019 [0.94-1.10]

1.04E-04

21

CHODL/ PRSS7

rs2248200

C/T

0.484

0.4815

0.598

1.01 [0.96-1.07]

1.35E-03

21

CHODL/PRSS7

rs1688165

A/G

0.485

0.4820

0.628

1.01 [0.96-1.07]

8.62E-04

16

ZNF423

rs1477020

T/C

0.121

0.1235

0.649

0.97 [0.86-1.10]

8.30E-06

1

C1QB

rs631090

C/T

0.073

0.0702

0.729

1.02 [0.90-1.15]

3.73E-04

16

ZNF423

rs1990629

G/A

0.128

0.1308

0.736

0.98 [0.87-1.10]

2.13E-05

11

OPCML

rs11223273

T/C

0.275

0.2721

0.759

1.01 [0.92-1.10]

1.40E-04

19

TSPAN16

rs322151

T/C

0.252

0.2527

0.990

0.99 [0.94-1.06]

3.37E-04

  1. N, 2,921 SSc/6,963 controls. aOdds ratio for the minor allele. Chr, chromosome; CI, confidence interval; MAF, minor allele frequency; OR, odds ratio; PBD, Breslow–Day test P value; PMH, allelic Mantel-Haenszel fixed effects model P value; SNP, single nucleotide polymorphism.