Table 1 Disease-associated SNPs identified through subset-selected FDR (ssFDR) < 0.01 amongst driver SNPs belonging to disease-significant components. Genes listed are nearby genes previously mentioned in the literature for the listed disease or basis diseases associated to this SNP, and are intended to indicate location; no evidence for gene causality has been assessed here. Where no basis diseases are associated with the SNP at genome-wide significant threshold (GWsig, p < 5 × 10−8), the strongest association and its p value are shown
Disease | SNP | Chrm | Position | p value | FDR | Genes | Basis diseases | Notes |
|---|---|---|---|---|---|---|---|---|
Genome-wide significant (4) | ||||||||
JIA RF− | rs2476601 | 1 | 114,377,568 | 2.36E−13 | 7.68E−11 | PTPN22 | CD, RA, SLE, T1D, VIT | |
EGPA combined | rs13405741 | 2 | 111,913,056 | 2.89E−09 | 1.07E−06 | BCL2L11 | PSC | |
EGPA ANCA− | rs11745587 | 5 | 131,796,922 | 3.59E−08 | 1.33E−05 | IRF1/IL5 | Asthma, CD | |
JIA RF− | rs11065987 | 12 | 112,072,424 | 1.87E−08 | 2.81E−06 | SH2B3 | PBC, T1D, VIT | |
Genome-wide significant in another subtype or study (7) | ||||||||
JIA PO | rs2476601 | 1 | 114,377,568 | 7.59E−06 | 3.65E−03 | PTPN22 | CD, RA, SLE, T1D, VIT | RF− subtype of JIA |
Myasthenia gravis combined | rs2476601 | 1 | 114,377,568 | 6.62E−05 | 2.61E−03 | PTPN22 | CD, RA, SLE, T1D, VIT | GWsig in myasthenia gravis |
EGPA ANCA− | rs13405741 | 2 | 111,913,056 | 1.33E−06 | 2.46E−04 | BCL2L11 | PSC | GWsig in EGPA combined |
JIA EO | rs7574865 | 2 | 191,964,633 | 7.77E−07 | 1.24E−04 | STAT4 | PBC, RA, SLE | GWsig in JIA combined |
Myasthenia gravis combined | rs231804 | 2 | 204,708,646 | 8.57E−07 | 1.69E−04 | CTLA4 | RA, T1D | r2 > 0.5 with non-driver SNP rs231770, p = 3.98E−08 |
Myasthenia gravis late onset | rs231804 | 2 | 204,708,646 | 1.18E−05 | 2.33E−03 | CTLA4 | RA, T1D | r2 > 0.5 with non-driver SNP rs231770, p = 3.98E−08 |
JIA RF− | rs1893217 | 18 | 12,809,340 | 1.69E−06 | 1.10E−04 | PTPN2 | CD, RA, T1D | GWsig in JIA combined |
Supported by other evidence in another study (5) | ||||||||
EGPA combined | rs11745587 | 5 | 131,796,922 | 3.44E−07 | 6.38E−05 | IRF1, IL5 | Asthma, CD | GWsig conditional on asthma GWAS |
EGPA combined | rs6454802 | 6 | 90,814,199 | 8.73E−06 | 6.48E−04 | BACH2 | Asthma, T1D, VIT | GWsig conditional on eosinophil count GWAS |
EGPA ANCA− | rs6454802 | 6 | 90,814,199 | 1.23E−05 | 1.52E−03 | BACH2 | Asthma, T1D, VIT | GWsig conditional on eosinophil count GWAS |
EGPA combined | rs8179 | 7 | 92,236,164 | 6.05E−06 | 5.61E−04 | CDK6 | RA 4.3e−07 | GWsig conditional on eosinophil count GWAS |
EGPA ANCA− | rs8179 | 7 | 92,236,164 | 5.51E−05 | 3.34E−03 | CDK6 | RA 4.3e−07 | GWsig conditional on eosinophil count GWAS |
Not previously reported (8) | ||||||||
JIA RF− | rs9594746 | 13 | 42,989,660 | 1.06E−05 | 4.91E−04 | TNFSF11 | PBC 4.7e−07 | r2 = 0.9 with rs34132030 (p = 2 × 10−7 in larger dataset [25]) |
EGPA combined | rs12405671 | 1 | 117,263,868 | 2.99E−06 | 3.70E−04 | CD2, CD28 | RA 1e−07 | |
EGPA ANCA− | rs12405671 | 1 | 117,263,868 | 4.06E−05 | 3.04E−03 | CD2, CD28 | RA 1e−07 | |
EGPA combined | rs1457115 | 5 | 110,567,598 | 3.21E−05 | 1.98E−03 | TSLP, WDR36, CAMK4 | Asthma | NB unlinked to nearby and previously reported EGPA-associated rs1837253 (r2 = 0.01) |
EGPA ANCA− | rs1457115 | 5 | 110,567,598 | 2.16E−04 | 8.01E−03 | TSLP, WDR36, CAMK4 | Asthma | NB unlinked to nearby and previously reported EGPA-associated rs1837253 (r2 = 0.01) |
Myasthenia gravis combined | rs2188962 | 5 | 131,770,805 | 3.78E−05 | 2.61E−03 | IRF1, IL5 | Asthma, CD | |
Myasthenia gravis late onset | rs2188962 | 5 | 131,770,805 | 6.01E−05 | 5.95E−03 | IRF1, IL5 | Asthma, CD | |
EGPA combined | rs10876864 | 12 | 56,401,085 | 1.19E−04 | 4.42E−03 | SUOX, IKZF4 | T1D, VIT | |