Table 1

Non-HLA index SNPs passing study suggestive significance threshold (5×10-6) and genome-wide significance threshold

SNPChr.Position (bp)Notable genesRisk/non-risk alleleRAFHWE (cases)HWE (controls)P valueOR95% CI
rs6679677 1 114 303 808 RSBN1; PTPN22 A/C 0.1 0.19 0.35 9.18E-14 1.36 1.24 to 1.48
rs7731626 5 55 444 683 ANKRD55 G/A 0.63 0.27 0.38 1.76E-13 1.22 1.15 to 1.3
rs11889341 2 191 943 742 STAT4 T/C 0.22 0.96 1 1.83E-10 1.24 1.16 to 1.32
rs4766578 12 111 904 371 ATXN2 T/A 0.49 0.21 0.13 3.03E-10 1.22 1.15 to 1.29
rs9960807 18 12 770 851 RP11-973H7.1;PTPN2 G/A 0.13 0.74 0.46 1.58E-09 1.26 1.16 to 1.36
rs34536443 19 10 463 118 TYK2 G/C 0.95 0.77 0.56 2.32E-09 1.53 1.31 to 1.79
rs497523 16 28 577 931 CLN3; CCDC101 T/C 0.65 0.94 0.03 7.12E-09 1.17 1.11 to 1.25
rs13160933555 545 859 NA C/T0.880.8416.49E-081.261.15 to 1.38
rs79815064346 277 577 CCR3 A/G0.870.450.67.61E-081.251.14 to 1.37
rs26142586135 677 202 AHI1 A/G0.380.20.229.17E-081.151.08 to 1.22
rs10515331469 259 662 ZFP36L1 A/C0.210.630.851.62E-071.21.12 to 1.28
rs1131715551738 296 272 CASC3 A/G0.020.730.142.92E-071.461.22 to 1.75
rs7270436898 894 396 PTPRD A/G0.050.760.644.14E-071.31.15 to 1.47
rs24810651154 311 911 ATP8B2; IL6R G/A0.110.320.876.11E-071.241.14 to 1.35
rs770114941624 333 566 CACNG3 A/G0.040.860.897.04E-071.411.23 to 1.6
rs73208061327 684 929 USP12 C/A0.090.860.127.36E-071.251.14 to 1.37
rs64343902191 262 762 INPP1; MFSD6 G/C0.480.050.547.42E-071.161.1 to 1.23
rs126548125176 794 191 RGS14 A/G0.340.220.647.61E-071.171.1 to 1.24
rs8400121167 414 872 CD247 C/T0.590.460.958.21E-071.151.08 to 1.22
rs127068607128 570 026 NA C/G0.650.60.138.78E-071.181.11 to 1.25
rs72043551658 951 694 RP11-410D17.2 G/T0.790.260.071.04E-061.191.1 to 1.28
rs706778106 098 949 IL2RA T/C0.40.340.781.28E-061.151.09 to 1.22
rs4869314596 229 225 ERAP2 G/T0.490.580.881.35E-061.141.08 to 1.21
rs70827201090 742 049 ACTA2 T/C0.450.60.661.67E-061.151.09 to 1.21
rs22221381812 889 217 PTPN2 G/T0.680.420.982.02E-061.171.1 to 1.24
rs15210883132 815 094 TMEM108 T/C0.020.740.062.08E-061.411.18 to 1.68
rs34173901333 087 914 GLB1 C/G0.150.30.652.13E-061.21.12 to 1.3
rs768701283138 211 845 CEP70 C/T0.970.570.532.66E-061.611.31 to 2
rs589231642144 158 451 PDE9A T/G0.04112.68E-061.341.17 to 1.53
rs134339143159 902 148 IL12A-AS1 C/G0.220.710.632.74E-061.171.09 to 1.25
rs23718872214 085 179 NA G/A0.430.330.972.79E-061.151.08 to 1.21
rs17175011014 354 673 FRMD4A C/A0.120.570.553.07E-061.231.13 to 1.34
rs1388156171719 445 425 SLC47A1 A/G0.010.613.28E-061.541.22 to 1.94
rs124303031343 032 027 TNFSF11 C/T0.450.40.573.61E-061.131.07 to 1.2
rs18671500041 589 324 NA G/A0.0110.273.72E-061.521.24 to 1.87
rs70435059117 628 528 TNFSF8 A/G0.550.470.253.74E-061.151.08 to 1.21
rs72657048125 289 734 RUNX3 G/C0.50.650.773.90E-061.141.08 to 1.21
rs7647909371 200 157 FOXP1 G/T0.240.130.64.56E-061.161.09 to 1.23
rs116928672100 759 477 AFF3 G/A0.640.530.64.57E-061.131.07 to 1.2
rs80136777345 931 005 CCR9 T/A0.880.570.24.68E-061.21.1 to 1.32
rs1395297144169 369 671 DDX60L C/T0.0110.274.78E-061.521.24 to 1.87
rs52178611129 607 371 NA C/A0.110.650.114.94E-061.191.09 to 1.3
rs66117111110 016 519 ZC3H12C G/T0.720.8204.95E-061.161.09 to 1.24
rs6506561188 233 559 PTPRM T/C0.550.860.15.00E-061.131.07 to 1.19
  • Genome-wide significant loci for juvenile idiopathic arthritis are highlighted in bold.

  • bp, base pair; Chr., chromosome; HLA, human leucocyte antigen; HWE, Hardy-Weinberg equilibrium; RAF, risk allele frequency; SNP, single nucleotide polymorphism.