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Table 2 Association finding for previously reported loci achieving P <0.01 in Immunochip, with findings in replication and overall datasets

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

SNP Chr Location (hg18; bp) Locus MAF cases MAF controls OR UnadjustedPvalue Replication OR ReplicationPvalue Combined analysis References
rs2056626 1 165,687,049 CD247 0.359 0.428 0.76 1.1 × 10−4 0.84 0.007 3.9 × 10−6 [6],[7],[11]
rs3821236 2 191,611,003 STAT4 0.255 0.194 1.41 2.6 × 10−5 1.24 0.008 1.2 × 10−6 [6],[7]
rs10168266 2 191,644,049 STAT4 0.249 0.190 1.40 4.1 × 10−5 1.30 0.001 1.9 × 10−7 [11]
rs7574865 2 191,672,878 STAT4 0.286 0.225 1.35 1.2 × 10−4 1.15 0.066 5.7 × 10−5 [7]
rs2176082 3 58,306,226 PXK 0.343 0.296 1.31 2.6 × 10−4 1.15 0.046 7.2 × 10−5 [16]
rs4728142 7 128,361,203 TNP03-IRF5 0.497 0.449 1.23 3.2 × 10−3 1.23 0.002 2.1 × 10−5 [6],[11]
rs10488631 7 128,381,419 TNP03-IRF5 0.156 0.114 1.50 2.4 × 10−5 1.36 0.001 1.6 × 10−7 [6],[7],[11]
rs12531711 7 128,404,702 TNP03-IRF5 0.156 0.113 1.51 2.1 × 10−5 1.38 0.001 8.6 × 10−8 [11]
rs1378942 15 72,864,420 CSK 0.379 0.319 1.27 8.7 × 10−4 1.17 0.023 7.8 × 10−5 [11]
  1. Chr chromosome; bp, base pairs; MAF, minor allele frequency; OR, odds ratio.