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Table 2 SLE risk SNPs association with clinical phenotypes

From: Genome-wide pathway analysis identifies VEGF pathway association with oral ulceration in systemic lupus erythematosus

SNP Chr Pos Gene RA Phenotype P D P V P C OR (CI, 95%)
rs2476601 a 1 114377568 PTPN22 A Hematologic disorder 0.0039 0.0433 5.20e-4 9.488 (1.310-68.726)
      Antinuclear antibodies 0.0146 0.0281 0.0011 0.168 (0.004-0.990)
rs704840 1 173226195 TNFSF4 G Renal disorder 0.0407 0.9210 0.1290 1.199 (0.941-1.527)
rs3024505 1 206939904 IL10 T Arthritis 0.0325 0.1540 0.0170 1.557 (1.091-2.221)
rs3768792 2 213871709 IKZF2 C Photosensitivity 0.0437 0.3320 0.4580 0.893 (0.674-1.184)
      Hematologic disorder 0.0319 0.1880 0.0143 0.507 (0.301-0.855)
rs9311676 3 58470351 ABHD6,PXK C Oral ulcers 0.0338 0.7960 0.9210 0.832 (0.674-1.028)
rs564799 3 159728987 IL12A C Discoid rash 0.0411 0.1410 0.6853 0.942 (0.674-1.316)
rs1270942 6 31918860 MHC class III C Arthritis 0.0138 0.6670 0.0407 1.530 (1.010-2.346)
rs9462027 6 34797241 UHRF1BP1 A Malar rash 0.0263 0.1730 0.0137 1.333 (1.071-1.660)
      Oral ulcers 0.0251 0.8950 0.0933 1.210 (0.971-1.508)
rs6932056 6 138242437 TNFAIP3 C Serositis 0.0193 0.8140 0.1364 1.580 (0.898-2.781)
rs4917014 7 50305863 IKZF1 T Oral ulcers 0.0280 0.1550 0.5821 0.944 (0.753-1.184)
rs2663052 10 50069395 WDFY4 C Neurologic disorder 0.0370 0.1590 0.6311 0.963 (0.662-1.401)
rs4948496 10 63805617 ARID5B C Malar rash 0.0331 0.4580 0.3258 1.116 (0.906-1.375)
      Photosensitivity 0.0202 0.9480 0.0911 1.203 (0.977-1.483)
rs2732549 11 35088399 CD44 T Immunologic disorder 0.0163 0.9910 0.0907 1.277 (0.976-1.670)
rs7941765 11 128499000 ETS1,FLI1 C Arthritis 0.0072 0.0701 0.0015 1.470 (1.151-1.877)
rs10774625 12 111910219 SH2B3 A Serositis 0.0207 0.0756 0.0038 0.715 (0.571-0.895)
      Renal disorder 0.0423 0.6410 0.0773 0.814 (0.650-1.018)
      Immunologic disorder 0.0051 0.8190 0.0321 0.738 (0.566-0.964)
rs1059312 12 129278864 SLC15A4 C Serositis 0.0253 0.2370 0.0156 1.321 (1.053-1.658)
rs4902562 14 68731458 RAD51B A Renal disorder 0.0130 0.8670 0.1010 0.834 (0.664-1.047)
rs2941509 17 37921194 IKZF3 A Antinuclear Antibodies 0.0304 0.0413 0.4943 0.676 (0.237-1.930)
rs2304256 19 10475652 TYK2 C Arthritis 0.0298 0.7690 0.1841 0.826 (0.622-1.096)
  1. A total of 19 SLE risk genetic variants were significantly associated with different systemic lupus erythematosus (SLE) phenotypes in the discovery stage. From these, the association between PTPN22 and hematologic disorder and between PTPN22 and the production of antinuclear antibodies (a) were significantly replicated in the validation cohort. Combining the statistical evidence from the two cohorts, seven additional genetic variants were found to be nominally associated with SLE phenotypes (shown in bold). Abbreviations: SNP single-nucleotide polymorphism, Chr chromosome, Pos SNP base pair in build GRCh37/hg19, RA disease risk allele, P D P value discovery cohort, P V P value validation cohort, P C P value combined, OR odds ratio according to the allele associated with disease risk, CI confidence interval (95%)