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Table 1 SNPs associated with SSc ( P <10 −4.5 ) in an analysis of Immunochip genotypes for 486 cases and 4,458 controls, replication cohort of 700 SSc cases (220 ACA positive) and 1,889 controls, and combined

From: An Immunochip-based interrogation of scleroderma susceptibility variants identifies a novel association at DNASE1L3

Chr

Location range (base pairs, hg18)

Best SNP

MAF cases

MAF controls

Immunochip OR

ImmunochipPvalue

Replication OR

ReplicationPvalue

Combined analysis

Gene annotation#

6

32,039,116-32,888,448

rs2857130

0.293

0.389

0.68

2.8 × 10−7

0.81

0.003

1.3 × 10−8

Intergenic (HLA region)

1

101,009,225

Novel SNP

0.024

0.008

3.31

1.8 × 10−6

2.49

0.031

1.9 × 10−7

Intergenic (VCAM1)

3

58,158,676-58,289,303

rs35677470

0.122

0.083

1.63

3.4 × 10−6

1.27

0.027

1.2 × 10−6

DNASE1L3 (coding)

3

58,158,676-58,289,303

rs35677470

0.174

0.083

2.36

2.3 × 10−10

1.74

3.0 × 10−4

8.71 × 10−13

DNASE1L3 (coding)^

7

128,372,852-128,499,110

rs34381587

0.158

0.113

1.53

1.2 × 10−5

1.38

8.7 × 10−4

5.2 × 10−8

IRF5/TNPO3 (intron)

16

73,863,956-74,046,823

rs11149824

0.469

0.391

1.35

1.4 × 10−5

1.054

0.442

3.2 × 10−4

CFDP1 (intron)

2

43,775,459-43,784,213

rs13403030

0.384

0.318

1.36

1.5 × 10−5

0.92

0.242

0.027

PLEKHH2 (intron)

2

191,608,694-191,641,499

rs13426947

0.253

0.191

1.42

1.8 × 10−5

1.25

5.4 × 10−3

6.1 × 10−7

STAT4 (intron)

1

61,883,642

rs2886326

0.249

0.195

1.41

2.0 × 10−5

0.96

0.606

7.4 × 10−3

Intergenic (TM2D1)

  1. #Gene annotation is based on the location of the most significant SNP; ^ACA-positive cases only. SNP, single nucleotide polymorphism; SSc, systemic sclerosis; ACA, anti-centromere antibody; Chr, chromosome; MAF, minor allele frequency; OR, odds ratio.