Table 2

Details of 18 confirmed RA susceptibility gene SNPs selected for genotyping

GeneSNPChrbpReason for selection
AFF3rs108650352100202166Most associated T1D SNP associated with RA15
AFF3rs11605422100198587rs10865035 proxy (r2=0.967)
STAT4rs75748652191672878Strongest association in US and UK studies10–12
STAT4rs1018165662191678124rs7574865 proxy (r2=0.951)
CTLA4rs2317752204440959+49 exon 17 A→G SNP, implicated in autoimmunity15
CTLA4rs30872432204447164Associated in US population7 15
IL2/IL21 locusrs68228444123728871Most associated celiac disease SNP, associated with T1D and RA7 14 15
TNFAIP3rs132070336138007111Most strongly associated SNP in US study9
TNFAIP3rs131928416138008907rs13207033 proxy (r2=1); second US SNP9
TNFAIP3rs69202206138048197Most strongly associated SNP in UK study8
TNFAIP3rs50299376138236844Intron 2 SNP
CCL21rs2812378934700260Most strongly associated SNP at locus7
TRAF1rs107601309122741811Most strongly associated UK SNP11
TRAF1rs29001809122746203Most strongly associated US SNP13
PRKCQrs4750316106433266Most associated SNP at locus16
KIF5Ars16785421256254982Most strongly associated SNP at locus16
CD226rs7633611865682622Most associated T1D SNP, associated with MS, AITD and RA17
CD40rs48104852044181354Most 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.