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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.