Single nucleotide polymorphism (SNP) markers and their proxys for the independent rheumatoid arthritis susceptibility loci considered for analysis. The shared epitope is not defined by SNP markers, but by a list of 4-digit HLA-DRB1 alleles described in the methods section
| Chromosome | Locus name | Single nucleotide polymorphism markers | ||
|---|---|---|---|---|
| 1 | CD2/CD58 | rs11586238 | ||
| 1 | FCGR2A | rs12746613 | rs10494360 | |
| 1 | MMEL1/TNFRSF14 | rs10910099 | rs3890745 | |
| 1 | PTPN22 | rs2476601 | rs6679677 | |
| 1 | PTPRC | rs10919563 | rs1932435 | |
| 2 | AFF3 locus 1 | rs1160542 | rs11676922 | rs9653442 |
| 2 | AFF3 locus 2 | rs10865035 | ||
| 2 | CD28 | rs1980422 | ||
| 2 | CTLA4 | rs3087243 | rs231804 | |
| 2 | REL | rs13031237 | ||
| 2 | SPRED2 | rs934734 | rs17534670 | |
| 2 | STAT4 | rs7574865 | ||
| 3 | DNASE1L3/PXK | rs13315591 | rs9813011 | |
| 4 | IL2/IL21 | rs6822844 | rs13151961 | |
| 4 | RBPJ | rs874040 | rs10517086 | |
| 5 | ANKRD55/IL6ST | rs6859219 | ||
| 5 | GIN1/C5orf30 | rs26232 | rs35797 | |
| 6 | CCR6 | rs3093023 | rs6907666 | rs3093024 |
| 6 | HLA-DRB1 0401 tag | rs6910071 | ||
| 6 | PRDM1 | rs548234 | ||
| 6 | TAGAP | rs394581 | rs169858 | |
| 6 | TNFAIP3 locus 1 | rs6920220 | rs2327832 | |
| 6 | TNFAIP3 locus 2 | rs13207033 | rs10499194 | |
| 6 | TNFAIP3 locus 3 | rs5029937 | rs5029939 | |
| 7 | IRF5 | rs10488631 | rs12531711 | |
| 8 | BLK | rs2736340 | ||
| 9 | CCL21 locus 1 | rs951005 | ||
| 9 | CCL21 locus 2 | rs2812378 | rs10814138 | |
| 9 | TRAF1/C5 | rs3761847 | ||
| 10 | IL2RA locus 1 | rs706778 | rs10795791 | rs7072793 |
| 10 | IL2RA locus 2 | rs2104286 | ||
| 10 | PRKCQ | rs4750316 | rs10796045 | |
| 11 | RAG1/TRAF6 | rs540386 | rs5030437 | rs1046864 |
| 12 | KIF5A/PIP4K2C | rs1678542 | rs11172254 | |
| 20 | CD40 | rs4810485 | rs1569723 | |
| 22 | IL2RB | rs3218253 | rs3218258 | |