Table 1

Twenty-six independent variants associated at a genome-wide significance level (p<5×10−8) in the meta-analysis

ChrPosition*SNPGene†Functionality‡Effect alleleOR (95% CI)Meta-analysis p value§Cochran’s p valueContributing
disease¶
167802371rs6659932 IL12RB2 IntronicC0.85 (079 to 0.91)6.08×10–11 1.02×10–02 IIM, SLE, SSc
1114303808rs6679677 PHTF1- RSBN1 IntergenicA1.34 (1.21 to 1.49)2.30×10–28 2.14×10–04 IIM, RA, SLE
1114377568rs2476601 PTPN22 Coding (missense)G0.75 (0.67 to 0.83)1.74×10–28 1.06×10–4 IIM, RA, SLE
1114433946rs1217393 AP4B1 IntronicA0.89 (0.85 to 0.92)5.21×10–09 4.91×10–1 IIM, RA, SLE, SSc
1173337747rs2422345 TNFSF4-LOC100506023 IntronicA1.11 (1.05 to 1.18)2.55×10–08 6.00×10–03 IIM, SLE, SSc
1183532580rs17849502 NCF2 Coding (missense)T1.36 (1.16 to 1.59)3.93×10–15 2.84×10–04 IIM, SLE
2191564757rs744600 NAB1 ** 3’DownstreamT0.88 (0.85 to 0.92)7.07×10–11 7.60×10–1 IIM, RA, SLE, SSc
2191933283rs13389408 STAT4 IntronicC1.27 (1.20 to 1.34)3.10×10–17 3.99×10–1 IIM, SLE, SSc
2191973034rs10174238 STAT4 IntronicA0.73 (0.67 to 0.80)2.76×10–42 4.31×10–07 IIM, SLE, SSc
358183636rs35677470 DNASE1L3 Coding (missense)A1.22 (1.14 to 1.30)4.96×10–09 6.78×10–01 IIM, SLE, SSc
3160312921rs112846137 KPNA4-ARL14 **  IntergenicT1.27 (1.17 to 1.37)1.42×10–08 9.55×10–01 IIM, RA, SLE, SSc
4965720rs13101828 DGKQ ** IntronicG1.11 (1.07 to 1.16)1.32×10–08 2.29×10–01 IIM, RA, SLE, SSc
5150438477rs4958880  TNIP1 IntronicA1.16 (1.10 to 1.22)1.45×10–11 2.61×10–01 IIM, RA, SLE, SSc
5159887336rs2431098 PTTG1-MIR3142HG IntergenicG1.12 (1.05 to 1.20)4.91×10–12 1.42×10–01 SLE, SSc
6106569270rs802791 PRDM1-ATG5 IntergenicC0.87 (0.83 to 0.92)3.65×10–12 1.13×10–01 SLE, SSc
6138243739rs58721818 TNFAIP3 3’DownstreamT1.64 (1.46 to 1.84)4.64×10–23 1.65×10–01 IIM, SLE, SSc
773537902rs193107685 LIMK1 ** 3’DownstreamC1.52 (1.27 to 1.83)3.21×10–09 1.18×10–01 RA, SLE, SSc
7128589633rs10954214 IRF5 3UTRT1.18 (1.13 to 1.23)6.63×10–17 3.64×10–01 IIM, RA, SLE, SSc
7128647942rs13238352 TNPO3 IntronicT1.44 (1.30 to 1.60)1.47×10–38 2.12×10–01 SLE, SSc
811341880rs2736337 FAM167A-BLK IntergenicC1.23 (1.17 to 1.30)4.86×10–22 1.29×10–01 IIM, RA, SLE, SSc
116 33 689rs7929541 SCT-DRD4 IntergenicG0.89 (0.83 to 0.95)2.14×10–10 4.98×10–04 IIM, RA, SLE, SSc
12112871372rs11066301 PTPN11 IntronicT1.11 (1.07 to 1.15)4.20×10–08 5.86×10–01 IIM, SLE, SSc
1685994484rs35929052 IRF8 IntergenicT0.83 (0.78 to 0.88)1.71×10–09 4.69×10–01 IIM, SLE, SSc
1910462513rs11085725 TYK2 IntronicA0.88 (0.83 to 0.92)2.65×10–10 1.86×10–01 IIM, SLE, SSc
1950121274rs76246107 PRR12 ** IntronicG1.28 (1.14 to 1.43)3.36×10–08 1.50×10–02 IIM, SLE, SSc
2221985094rs5754467 YDJC 5’UpstreamG1.20 (1.13 to 1.27)1.24×10–13 8.59×10–02 IIM, RA, SLE, SSc
  • All the variants in the table were imputed in at least one of the 18 case-control collections.

  • *According to NCBI build GRCh37/hg19.

  • †Variant localisation based on the nearest gene.

  • ‡Functionality obtained from SNPnexus.23

  • §Results of meta-analysis either under a fixed effect if no heterogeneity was found based on Cochran’s Q test (p≥0.05) or under a random effect if heterogeneity was found among studies.

  • ¶Disease contributing to the association observed by the subset meta-analysis method with ASSET.25 The diseases for which this locus has never been reported before at genome-wide significance level are shown in boldface.

  • **Denotes novel loci in the study.