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Table 3 Validation of selected SNPs on the X chromosome in the central region

From: Discovery of a novel genetic susceptibility locus on X chromosome for systemic lupus erythematosus

 

Discovery set (central)a

Central validationb

 

Meta (discovery + central validation)c

Marker

Minor allele

Position (Hg19)

Annotation

Gene symbol

PVAL

OR

MAF case

MAF control

PVAL

OR

MAF case

MAF control

PVAL (FE)

PVAL (RE)

OR (FE)

OR (RE)

I 2

PVAL (Het)

rs5914778

A

56758231

Intronic

LINC01420

3.59 × 10–3

1.29

0.286

0.238

7.15 × 10–7

1.33

0.296

0.24

1.00 × 10–8

1.00 × 10–8

1.32

1.32

0

7.58 × 10–1

rs1527803

A

16421982

184 kb 3′ of CTPS2

NA

6.75 × 10–2

0.87

0.368

0.402

1.90 × 10–2

1.13

0.403

0.374

3.63 × 10–1

9.82 × 10–1

1.04

1.00

87.5

4.70 × 10–3

rs5963635

A

39166975

None

LOC286442

1.40 × 10–3

1.34

0.247

0.197

2.17 × 10–1

1.08

0.230

0.217

5.17 × 10–3

1.08 × 10–1

1.15

1.19

74.1

4.94 × 10–2

rs1860995

G

119502122

Intronic

ATP1B4

7.48 × 10–4

1.30

0.417

0.355

6.74 × 10–1

1.02

0.395

0.389

1.69 × 10–2

2.87 × 10–1

1.10

1.11

81.4

4.33 × 10–2

rs2536576

G

147417249

165 kb 5′ of AFF2

NA

5.73 × 10–3

1.34

0.172

0.134

9.43 × 10–1

1.01

0.152

0.152

1.12 × 10–1

3.36 × 10–1

1.10

1.15

80.2

2.45 × 10–2

rs17326228

G

106239318

Intronic

MORC4

2.56 × 10–4

1.33

0.438

0.370

3.01 × 10–1

0.95

0.418

0.432

3.82 × 10–1

6.14 × 10–1

1.02

1.05

88.5

1.75 × 10–3

rs17329976

G

142130195

8.1 KB 3′ of SPANXN4

NA

4.28 × 10–2

0.83

0.179

0.209

1.58 × 10–1

0.91

0.160

0.174

2.23 × 10–2

3.62 × 10–2

0.85

0.83

51.6

1.62 × 10–1

rs5936901

G

67975499

30 kb 3′ of STARD8

NA

4.45 × 10–4

1.33

0.371

0.308

5.53 × 10–1

0.97

0.342

0.350

1.28 × 10–1

4.50 × 10–1

1.07

1.13

90.3

1.30 × 10–3

rs10218247

A

83476018

33 kb 5′ of RPS6KA6

NA

3.67 × 10–3

0.78

0.241

0.289

5.47 × 10–1

0.96

0.248

0.255

2.85 × 10–2

3.06 × 10–1

0.91

0.86

82.4

1.24 × 10–2

rs5970959

G

22987793

30 kb 5′ of DDX53

DDX53

1.42 × 10–2

1.25

0.254

0.215

1.57 × 10–1

0.92

0.251

0.267

3.76 × 10–1

6.41 × 10–1

1.03

1.05

86.7

2.06 × 10–3

rs6631753

A

33199451

Intronic

DMD

6.94 × 10–3

0.81

0.376

0.426

5.09 × 10–1

1.04

0.374

0.366

7.12 × 10–2

4.69 × 10–1

0.93

0.91

89.2

4.35 × 10–3

rs2411864

G

16377763

206 kb 3′ of GRPR

NA

5.04 × 10–3

0.76

0.154

0.194

4.81 × 10–1

1.05

0.165

0.159

2.98 × 10–1

5.16 × 10–1

0.94

0.90

86.2

7.10 × 10–3

  1. aFrom Han et al. [13] with 1017 cases and 539 controls from central China
  2. bConsists of 1156 cases and 2330 controls
  3. cConsists of 2173 cases and 2869 controls
  4. FE fixed effects, Het heterogeneity, I 2 heterogeneity statistic, MAF minor allele frequency, NA not available, OR odds ratio, PVAL P value, RE random effects, SNP single nucleotide polymorphism