Evaluation of SLE Susceptibility Genes in Malaysians

Table 1

SLE susceptibility genes in Malay (MA) and Chinese (CH).

Gene

Cytogenetic band

SNP

Base position

A1/A2

Chinese

Malay

Meta-analysis 𝑃 value*

F_A

F_U

𝑃 value

OR; 95% CI

F_A

F_U

𝑃 value

OR; 95% CI

TNFSF4-LOC730070

1q25

rs10798269

173,309,713

A/G

0.342

0.401

3.87×10^−2

0.78 (0.61–0.99)

0.314

0.460

1.88×10^−2

0.54 (0.32–0.9)

5.98×10^−3

NCF2

1q25

rs13306575

183,532,437

T/C

0.080

0.043

8.11×10^−3

1.95 (1.18–3.22)

0.119

0.070

1.93×10^−1

1.78 (0.74–4.28)

1.17×10^−2

MAPKAPK2-IL10

1q31-32

rs2232360

207,040,659

A/G

0.328

0.351

3.98×10^−1

0.9 (0.71–1.15)

0.576

0.397

5.06×10^−3

2.07 (1.24–3.45)

—

RASGRP3

2p25.1-24.1

rs13425999

33,702,203

T/C

0.129

0.174

3.03×10^−2

0.7 (0.51–0.97)

0.102

0.203

2.79×10^−2

0.44 (0.21–0.93)

6.82×10^−3

IFIH1

2q24

rs13023380

163,154,363

A/G

0.010

0.002

5.56×10^−2

6.14 (0.74–51.13)

0.025

0.103

1.42×10^−2

0.23 (0.06–0.82)

—

STAT4

2q32.2-32.3

rs7568275

191,966,452

G/C

0.453

0.317

2.88×10^−6

1.78 (1.4–2.27)

0.422

0.236

2.99×10^−3

2.36 (1.33–4.19)

1.68×10^−7

BANK1

4q24

rs17031870

102,940,788

G/A

0.092

0.058

2.89×10^−2

1.64 (1.05–2.56)

0.237

0.143

5.95×10^−2

1.87 (0.97–3.59)

1.26×10^−2

TNIP1

5q32-33.1

rs3792782

150,456,677

C/T

0.214

0.247

1.81×10^−1

0.83 (0.63–1.09)

0.305

0.453

1.70×10^−2

0.53 (0.31–0.89)

2.09×10^−2

HLA-DRA

6p21.3

rs6911777

32,409,996

C/T

0.264

0.137

6.57×10^−8

2.26 (1.67–3.05)

0.161

0.055

6.73×10^−3

3.32 (1.34–8.21)

9.96×10^−9

PRDM1-ATG5

6q21

rs9398065

106,546,034

C/G

0.075

0.039

9.52×10^−3

1.97 (1.17–3.31)

0.119

0.039

1.95×10^−2

3.31 (1.15–9.5)

1.78×10^−3

TNFAIP3

6q23

rs5029928

138,189,942

T/C

0.083

0.046

1.02×10^−2

1.88 (1.15–3.05)

0.059

0.031

2.87×10^−1

1.96 (0.56–6.86)

2.00×10^−2

C7orf721-IKZF1

7p13-11.1

rs11185603

50,306,810

G/C

0.236

0.282

7.61×10^−2

0.79 (0.61–1.03)

0.144

0.302

3.25×10^−3

0.39 (0.21–0.74)

2.30×10^−3

BLK

8p23-22

rs11782375

11,294,934

C/T

0.277

0.380

1.88×10^−4

0.62 (0.49–0.8)

0.297

0.375

1.94×10^−1

0.7 (0.41–1.2)

4.09×10^−4

LYN

8q13

rs7828258

56,867,945

T/C

0.223

0.242

4.38×10^−1

0.9 (0.68–1.18)

0.136

0.281

5.18×10^−3

0.4 (0.21–0.77)

1.61×10^−2

KIAA1542-PHRF1

11p15.5

rs4963128

589,564

T/C

0.083

0.070

4.01×10^−1

1.2 (0.78–1.86)

0.059

0.156

1.51×10^−2

0.34 (0.14–0.84)

—

IRF7

11p15.5

rs7943546

612,148

C/T

0.024

0.033

3.99×10^−1

0.74 (0.37–1.49)

0.025

0.055

2.46×10^−1

0.45 (0.11–1.79)

3.26×10^−1

PDHX-CD44

11p13

rs12362140

35,142,019

A/C

0.007

0.027

7.46×10^−3

0.25 (0.08–0.75)

0.085

0.148

1.22×10^−1

0.53 (0.24–1.2)

7.27×10^−3

ETS1

11q23.3

rs76404385

128,333,055

T/C

0.202

0.138

3.41×10^−3

1.59 (1.16–2.17)

0.178

0.063

5.02×10^−3

3.25 (1.38–7.65)

2.05×10^−4

SLC15A4

12q24.32

rs6486738

129,432,715

G/C

0.295

0.337

1.22×10^−1

0.82 (0.64–1.05)

0.203

0.305

6.90×10^−2

0.58 (0.32–1.05)

4.88×10^−2

IL21R

16p11

rs8060368

27,412,414

T/C

0.012

0.039

3.59×10^−3

0.3 (0.13–0.71)

0.170

0.109

1.72×10^−1

1.66 (0.8–3.46)

—

ITGAM

16p11.2

rs12444713

31,378,235

A/G

0.284

0.369

2.48×10^−3

0.68 (0.53–0.87)

0.5

0.52

7.10×10^−1

1.1 (0.67–1.82)

—

ORF8-LOC100131952

16q24.1

rs34912238

86,001,903

T/C

0.039

0.077

6.25×10^−3

0.49 (0.29–0.82)

0.076

0.031

1.15×10^−1

2.56 (0.77–8.55)

—

ICAM1-ICAM4

19p13.2

rs5498

10,395,683

G/A

0.250

0.267

5.06×10^−1

0.91 (0.7–1.19)

0.314

0.242

2.11×10^−1

1.43 (0.82–2.51)

—

TYK2

19p13.2

rs12975591

10,627,814

G/A

0.415

0.454

1.84×10^−1

0.85 (0.67–1.08)

0.232

0.121

2.62×10^−2

2.19 (1.09–4.41)

—

UBE2L3

22q11.21

rs2236642

21,989,621

T/C

0.089

0.127

3.61×10^−2

0.67 (0.46–0.98)

0.144

0.172

5.51×10^−1

0.81 (0.41–1.62)

9.77×10^−2

∗When ORs from CH and MA are in different directions, we did not perform the meta-analysis.
— indicated SNPs where no meta-analysis was performed.
OR: odds ratio. Minor allele frequencies are given for the minor allele A1. F_A: minor allele frequency for cases; F_U: minor allele frequency for controls.