Table 2.
Details of 18 confirmed RA susceptibility gene SNPs selected for genotyping
| Gene | SNP | Chr | bp | Reason for selection |
|---|---|---|---|---|
| AFF3 | rs10865035 | 2 | 100202166 | Most associated T1D SNP associated with RA15 |
| AFF3 | rs1160542 | 2 | 100198587 | rs10865035 proxy (r2=0.967) |
| STAT4 | rs7574865 | 2 | 191672878 | Strongest association in US and UK studies10–12 |
| STAT4 | rs101816566 | 2 | 191678124 | rs7574865 proxy (r2=0.951) |
| CTLA4 | rs231775 | 2 | 204440959 | +49 exon 17 A→G SNP, implicated in autoimmunity15 |
| CTLA4 | rs3087243 | 2 | 204447164 | Associated in US population7,15 |
| IL2/IL21 locus | rs6822844 | 4 | 123728871 | Most associated celiac disease SNP, associated with T1D and RA7,14,15 |
| TNFAIP3 | rs13207033 | 6 | 138007111 | Most strongly associated SNP in US study9 |
| TNFAIP3 | rs13192841 | 6 | 138008907 | rs13207033 proxy (r2=1); second US SNP9 |
| TNFAIP3 | rs6920220 | 6 | 138048197 | Most strongly associated SNP in UK study8 |
| TNFAIP3 | rs5029937 | 6 | 138236844 | Intron 2 SNP |
| CCL21 | rs2812378 | 9 | 34700260 | Most strongly associated SNP at locus7 |
| TRAF1 | rs10760130 | 9 | 122741811 | Most strongly associated UK SNP11 |
| TRAF1 | rs2900180 | 9 | 122746203 | Most strongly associated US SNP13 |
| PRKCQ | rs4750316 | 10 | 6433266 | Most associated SNP at locus16 |
| KIF5A | rs1678542 | 12 | 56254982 | Most strongly associated SNP at locus16 |
| CD226 | rs763361 | 18 | 65682622 | Most associated T1D SNP, associated with MS, AITD and RA17 |
| CD40 | rs4810485 | 20 | 44181354 | Most strongly associated SNP at locus7 |
A1TD, autoimmune thyroid disease; bp, base pairs; Chr, chromosome; MS, multiple sclerosis; RA, rheumatoid arthritis; SNP, single nucleotide polymorphism; T1D, type 1 diabetes.