Table 1.
Non-HLA candidate causal variants for SLE and AI disease risk genes/haplotypes
| Reported Gene/Haplotype | SNP | Chr | Pos (Mbp) | Typea | Reference | Alt | Ref log2FC | Alt log2FC | AE log2FC | −log10 FDR | Index SNP diseaseb | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SLE risk haplotype effects | RASGRP3 | rs13385731 | 2 | 33.48 | A | T | C | 0.22 | 1.72 | 1.50 | 1.77 | SLE |
| NEMP2-NAB1 | rs7608180 | 2 | 190.58 | D | G | T | 1.67 | 0.86 | −0.81 | 2.63 | novel | |
| PTTG1-miR146A | rs2431697 | 5 | 160.45 | A | T | C | 0.25 | 0.70 | 0.45 | 1.55 | SLE | |
| IRF5 | rs4728142 | 7 | 128.93 | A | G | A | 0.62 | 1.79 | 1.17 | 2.27 | SLE; MS; RA; UC |
|
| BLK | rs1564267 | 8 | 11.48 | I | T | C | 1.44 | 0.49 | −0.94 | 2.63 | novel | |
| BLK | rs2618476 | 8 | 11.50 | A & C | T | C | 1.27 | 0.56 | −0.71 | 2.03 | SLE | |
| PKIA-ZC2HC1A | rs3808619 | 8 | 78.67 | C | A | C | 0.39 | 1.47 | 1.08 | 3.10 | novel | |
| RNASEH2C-OVOL1 | rs12293022 | 11 | 65.76 | E | C | T | 0.57 | 1.27 | 0.70 | 1.44 | novel | |
| RNASEH2C-OVOL1 | rs10791824 | 11 | 65.79 | C | A | G | 1.99 | 1.29 | −0.70 | 1.42 | novel | |
| PHLDB1-DDX6-CXCR5 | rs658676 | 11 | 118.70 | F | C | T | 2.23 | 1.43 | −0.81 | 3.31 | novel | |
| GPR19 | rs10845606 | 12 | 12.68 | A | C | A | 0.68 | −0.12 | −0.80 | 1.64 | SLE | |
| CABP1-SPPL3 | rs510351 | 12 | 120.75 | E | A | G | −0.02 | 1.14 | 1.16 | 2.74 | novel | |
| SLC15A4 | rs35907548 | 12 | 128.80 | C | T | C | 3.70 | 1.51 | −2.18 | 2.26 | novel | |
| CIITA-SOCS1 | rs1985872 | 12 | 11.05 | G | G | C | 2.44 | 1.36 | −1.08 | 2.05 | novel | |
| CIITA-SOCS1 | rs7203793 | 16 | 11.09 | G | C | G | 0.99 | 0.02 | −0.97 | 1.57 | novel | |
| IRF8 | rs11117432 | 16 | 85.99 | A & C | G | A | 3.50 | 2.63 | −0.87 | 4.54 | SLE; PBC | |
| GRB2 | rs959260 | 17 | 75.37 | H | C | T | 0.17 | 0.75 | 0.58 | 1.96 | novel | |
| AI disease index SNPs | C5orf3 | rs26232 | 5 | 103.26 | B | C | T | 3.24 | 1.94 | −1.30 | 3.37 | RA |
| SLC22A23 | rs17309827 | 6 | 3.43 | B | T | G | 2.43 | 3.23 | 0.81 | 1.62 | CD | |
| IKZF1 | rs62447205 | 7 | 50.40 | B | A | G | 1.53 | 2.80 | 1.27 | 1.63 | T1D | |
| PVT1 | rs2019960 | 8 | 128.18 | B | T | C | 0.79 | 1.32 | 0.53 | 1.13 | MS | |
| IL2RA | rs12251307 | 10 | 6.08 | B | C | T | 2.76 | 0.46 | −2.30 | 2.44 | T1D | |
| GLYAT | rs11229555 | 11 | 58.64 | B | G | T | 1.79 | 1.46 | −0.33 | 1.88 | UC | |
| FADS1-FADS2 | rs968567 | 11 | 61.83 | B | C | T | 0.45 | 3.16 | 2.71 | 1.62 | RA; T1D | |
| ERBB3 | rs11171739 | 12 | 56.08 | B | C | T | 0.73 | 1.24 | 0.51 | 1.14 | T1D | |
| DLEU1 | rs9591325 | 13 | 50.24 | B | T | C | 2.32 | 2.80 | 0.47 | 2.16 | MS | |
| STAT3 | rs9891119 | 17 | 42.36 | B | A | C | 0.74 | 0.20 | −0.55 | 1.72 | CD; MS | |
| CD4 | rs4813003 | 20 | 46.13 | B | C | A,T | 0.0002 | 0.85 | 0.85 | 1.72 | KD | |
| CYCSP42 | rs2823286 | 21 | 15.45 | B | G | A | 1.12 | 1.47 | 0.36 | 1.21 | CD; UC | |
| UBE2L3 | rs2256609 | 22 | 21.57 | B | A | G | −0.09 | 0.67 | 0.76 | 1.52 | CD | |
| C1QTNF6 | rs229527 | 22 | 37.19 | B | C | A,G | 1.10 | 1.77 | 0.67 | 1.72 | GD; Vit |
The allele that demonstrates the allelic effect for each emVar is in italics. aType: A = SLE index SNP; B = AI index SNP; C = hQTL; D = hQTL proxy (r2 > 0.8); E = eQTL proxy (r2 > 0.8); F = haplotype SNP; G = proxy of SLE/AI index SNP (r2 > 0.8); H = suggestive AI index SNP (p < 1E−6); I = location control. bIndex SNP disease: CD = Crohn disease; GD = Graves’ disease; KD = Kawasaki disease; MS = multiple sclerosis; PBC = primary biliary cirrhosis; RA = rheumatoid arthritis; SLE = systemic lupus erythematosus; T1D = type 1 diabetes; UC = ulcerative colitis; Vit = vitiligo. Novel = variant not currently reported as an SLE index SNP (p < 5E−08) in the GWAS catalog.