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. 2022 Jan 27;44(1):47–62. doi: 10.1007/s00281-022-00912-0

Table 1.

Non-HLA genetic associations with rheumatoid arthritis by December 2021

SNP1 Chromosome: position2 Gene/Locus OR 95%CI Immune function ACPA Population3 Reference
rs2843401, rs3890745, rs2258734 1:2596694 MMEL1 0.91 (0.89–0.93) - Positive Asians, Europeans [46, 50, 51]
rs227163 1:7901146 TNFRSF9 1.04 (1.02–1.06) Yes Combined Asians [6]
rs2240336, rs2301888, esv3585367 1:17347907 PADI4 0.88 (0.86–0.90) Yes Combined Asians, Europeans [8, 46, 50]
rs28411352 1:37812907 MTF1 1.10 (1.07–1.13) - Combined Europeans, Trans Meta [6]
rs883220, rs7540342 1:38151199 POU3F1 0.89 (0.86–0.92) - Positive Europeans [8, 46]
rs41269479 1:41701111 HIVEP3 1.15 (1.09–1.20) Yes Positive Asians [8]
rs4655698 1:67332644 IL12RB2 1.09 (1.05–1.11) Yes Positive Trans Meta [8]
rs41313373 1:92474854 GFI1 1.12 (1.08–1.16) Yes Positive Europeans, Trans Meta [8]
rs2476601 1:113834946 PTPN22 1.81 (1.73–1.89) Yes Positive Europeans [43, 52]
rs11586238, rs798000, rs624988 1:116720516 CD2 1.12 (1.09–1.16) Yes Positive Europeans [8, 51]
rs2228145, rs12126142 1:154454494 IL6R 0.93 (0.91–0.95) Yes Combined Europeans, Trans Meta [6, 7, 46]
rs2317230, rs2317231 1:157705207 FCRL3 1.08 (1.05–1.10) Yes Positive Trans Meta [6]
rs12026490 1:160447367 SLAMF6 0.80 (0.75–0.85) Yes Combined Asians [7]
rs3753389 1:160837363 CD244 1.30 (1.18–1.43) Yes Combined Asians [53]
rs10917571 1:161549621 FCGR3A 0.91 (0.89–0.94) Yes Positive Trans Meta [8]
rs2105325, rs61828284, rs6681482 1:173380586 TNFSF4 1.12 (1.08–1.15) Yes Combined Europeans, Trans Meta [6, 8, 57]
rs10911902, rs12145329 1:186663185 PTGS2 0.92 (0.89–0.95) Yes Positive Trans Meta [7, 8]
rs28398409 1:198614892 PTPRC 0.91 (0.88–0.94) Yes Combined Trans Meta [8]
rs762574969 1:235637057 GNG4 0.91 (0.88–0.94) - Combined Europeans [8]
rs10175798 2:30226728 LBH 0.92 (0.90–0.94) Yes Combined Europeans, Trans Meta [6]
rs34695944, rs13031237 2:60897715 REL 1.12 (1.08–1.15) Yes Positive Europeans [6, 47]
rs11900673 2:62225526 B3GNT2 1.15 (1.08–1.21) Yes Combined Asians [50]
rs6546146, rs934734, rs1858037 2:65329190 SPRED2 0.90 (0.88–0.93) Yes Positive Asians, Europeans [50, 52]
rs143259280 2:69982037 PCBP1-AS1 1.09 (1.06–1.12) - Positive Trans Meta [8]
rs6705628 2:73981235 DGUOK-AS1 0.88 (0.85–0.92) - Combined Asians [7]
rs10209110, rs12712065 2:100056230 AFF3 1.10 (1.08–1.13) Yes Combined Asians, Europeans [8, 46, 52]
rs6732565 2:110850255 ACOXL 1.07 (1.05–1.10) - Combined Europeans, Trans Meta [6, 8]
rs13426947, rs7574865 2:191068528 STAT4 1.16 (1.13–1.19) Yes Combined Asians, Europeans [46, 50]
rs10497813 2:198049348 PLCL1-LINC01923 1.06 (1.04–1.09) - Combined Europeans, Trans Meta [8, 58]
rs6715284, rs2141331 2:201289674 CASP8 1.15 (1.10–1.20) Yes Combined Europeans, Trans Meta [6, 8]
rs1980422 2:203745673 CD28 1.12 (1.09–1.16) Yes Combined Europeans [51]
rs11571302, rs3087243 2:203878211 CTLA4 0.88 (0.86–0.90) Yes Positive Asians, Europeans [8, 52]
rs77574423 3:11943270 TAMM41-SYN2 0.89 (0.86–0.93) - Positive Europeans [8]
rs4452313, rs4602367 3:17005540 PLCL2 0.93 (0.91–0.95) Yes Combined Europeans, Trans Meta [6, 7]
rs3806624 3:27723132 EOMES 0.92 (0.89–0.94) Yes Combined Europeans, Trans Meta [6, 7]
rs73081554 3:58317208 DNASE1L3 1.18 (1.11–1.25) Yes Combined Europeans [6]
rs62264113 3:127573490 TPRA1 0.92 (0.89–0.95) - Combined Trans Meta [8]
rs9826828 3:136683218 IL20RB 1.44 (1.28–1.61) Yes Combined Europeans [6]
rs4687070 3:189588861 TPRG1-TP63 1.15 (1.09–1.20) - Combined Trans Meta [8]
rs4690029 4:2721088 FAM193A 0.94 (0.92–0.96) - Combined Trans Meta [8]
rs13142500, rs13103285 4:10725733 CLNK 1.10 (1.08–1.13) Yes Combined Asians, Trans Meta [6, 7]
rs932036, rs874040, rs11933540 4:26089240 RBPJ 1.15 (1.11–1.19) Yes Combined Europeans [6, 46, 52]
rs2664035 4:48218822 TEC 1.07 (1.04–1.10) Yes Combined Europeans [6]
rs2867461 4:78592061 ANXA3 1.13 (1.09–1.17) Yes Combined Asians [50]
rs950918814 4:80031255 ANTXR2 0.93 (0.91–0.95) - Combined Trans Meta [8]
rs58107865 4:108140462 LEF1 0.84 (0.80–0.88) Yes Combined Asians [8]
rs6814280 4:122122507 KIAA1109 0.93 (0.90–0.96) - Positive Europeans [8]
rs2918392 5:10704685 DAP 0.94 (0.91–0.96) Yes Combined Trans Meta, Europeans [7, 8]
rs56787183 5:40499188 PTGER4 0.85 (0.80–0.90) Yes Combined Trans Meta [8]
rs71624119, rs6859212, rs7731626 5:56144903 ANKRD55 0.82 (0.79–0.85) Yes Combined Asians, Europeans [7, 8, 46, 52]
rs71624119, rs7731626 5:56144903 ANKRD55 0.85 (0.80–0.91) Yes Negative Europeans [8, 46]
rs2561477, rs403214, rs187579 5:103273223 MACIR 1.10 (1.06–1.13) Yes Combined Europeans, Trans Meta [68, 52]
rs657075, rs244685 5:132094425 CSF2 1.09 (1.06–1.12) Yes Combined Asians, Trans Meta [7, 50]
rs244468 5:143224856 ARHGAP26 0.93 (0.91–0.95) - Combined Trans Meta [8]
rs1422673 5:151059427 TNIP1 1.10 (1.06–1.14) Yes Positive Europeans [8]
rs9378815, rs6930468 6:426155 IRF4 0.91 (0.89–0.94) Yes Combined Trans Meta [6, 8]
rs12529514, rs12530098 6:14096427 CD83 1.15 (1.10–1.20) Yes Combined Asians, Trans Meta [7, 50]
rs113532504 6:15195451 JARID2 1.13 (1.08–1.18) Yes Combined Europeans [8]
rs67318457 6:23924793 NRSN1 1.09 (1.05–1.12) - Positive Europeans [8]
rs2234067, rs11420145 6:36387877 ETV7 1.15 (1.10–1.20) Yes Combined Europeans, Trans Meta [6, 8]
rs2233424, rs28362855 6:44266184 POLR1C, NFKBE 1.22 (1.17–1.26) Yes Combined Asians, Europeans [6, 8, 50]
rs72928038 6:90267049 BACH2 1.09 (1.06–1.11) Yes Combined Europeans, Trans Meta [8, 23, 59]
rs548234, rs9372120, rs3804333 6:106120159 PRDM1-ATG5 1.11 (1.07–1.15) Yes Positive Asians, Europeans [6, 8, 51]
rs10499194, rs6920220, rs6932056, rs7752903 6:137681500 TNFAIP3 1.33 (1.26–1.40) Yes Positive Asians, Europeans [6, 46, 50, 60]
rs9373594 6:149513438 PPIL4 1.09 (1.06–1.12) Yes Combined Asians [6]
rs629326, rs2451258 6:159075681 TAGAP 1.11 (1.08–1.14) Yes Positive Europeans [6, 46]
rs59466457, rs3093023, rs1571878 6:167124266 CCR6 0.86 (0.84–0.88) Yes Positive Asians, Europeans [46, 50, 52]
rs940825 7:17167540 AGR3-AHR 1.13 (1.08–1.18) - Positive Europeans [8]
rs182199544 7:27044962 SKAP2-HOXA1 0.87 (0.84–0.91) Yes Positive Europeans [8]
rs67250450, rs740122 7:28135367 JAZF1 0.92 (0.90–0.95) - Combined Europeans, Trans Meta [6, 7]
rs6583441 7:50322278 IKZF1 0.95 (0.93–0.97) Yes Combined Trans Meta [8]
rs113066392, rs73366469 7:74611832 GTF2IRD1-NCF1 1.43 (1.33–1.55) Yes Combined Asians [7, 56, 61]
rs4272, rs42044 7:92607515 CDK6 0.92 (0.89–0.94) Yes Combined Europeans, Trans Meta [6, 8]
rs6979218 7:100295525 CASTOR3-SPDYE3 0.92 (0.89–0.94) - Combined Europeans, Trans Meta [8]
rs3807306, rs10488631 7:128940626 IRF5 0.88 (0.86–0.91) Yes Combined Asians, Europeans [46, 50, 52]
rs4840565, rs2736340 8:11488036 BLK 1.12 (1.09–1.15) Yes Combined Asians, Europeans [68, 47]
rs998731, rs10453119 8:80183160 TPD52 1.08 (1.05–1.11) - Combined Europeans, Trans Meta [6, 8]
rs678347, rs1264600 8:101451374 GRHL2 1.08 (1.05–1.11) - Combined Europeans, Trans Meta [6, 8]
rs1516971, rs16903108 8:128529854 PVT1 1.15 (1.10–1.20) - Combined Europeans, Trans Meta [6, 8]
rs11777380 8:133199722 CCN4 0.92 (0.90–0.95) - Combined Trans Meta [8]
rs911760 9:5438435 PLGRKT 1.15 (1.09–1.20) - Positive Europeans [8]
rs2812378, rs11574914 9:34710263 CCL21 1.12 (1.09–1.16) Yes Positive Europeans, Trans Meta [6, 8, 46, 52]
rs3761847, rs10985070 9:120927961 TRAF1-C5 0.92 (0.90–0.95) Yes Positive Europeans, Trans Meta [5, 6]
rs706778, rs3134883 10:6056986 IL2RA 1.10 (1.08–1.13) Yes Combined Europeans, Trans Meta [6, 7, 52]
rs947474, rs502919 10:6348488 PRKCQ 0.92 (0.90–0.94) Yes Combined Europeans, Trans Meta [6, 7]
rs2275806, rs3824660, rs10905284 10:8053377 GATA3 0.93 (0.91–0.95) Yes Positive Europeans, Trans Meta [6, 8, 46]
rs793108, rs793095, rs1538981 10:31126177 ZNF438 1.07 (1.05–1.09) - Combined Trans Meta [68]
rs2671692, rs7097397 10:48889774 WDFY4 0.92 (0.90–0.94) Yes Combined Asians, Trans Meta [68]
rs12764378, rs10821944, rs7902146 10:62040245 ARID5B 1.16 (1.13–1.19) Yes Positive Asians, Europeans [8, 46, 50]
rs6479800, rs3125734 10:62277122 RTKN2 1.11 (1.07–1.15) - Combined Asians, Trans Meta [6, 49]
rs726288 10:79947217 SFTPD 1.14 (1.07–1.20) Yes Combined Asians [6]
rs734094 11:2301990 TSPAN32 1.08 (1.05–1.10) Yes Positive Trans Meta [8]
rs9943599 11:9731194 SWAP70 1.09 (1.06–1.11) Yes Combined Asians, Trans Meta [7, 48]
rs595158, rs968567, rs7943728 11:61142109 FADS1-FADS2-FADS3 1.12 (1.07–1.16) - Combined Europeans [6, 8, 46]
rs660442, rs479777 11:64275525 BAD 0.90 (0.87–0.93) Yes Combined Asians, Trans Meta [7, 8]
rs59578717 11:69092402 TPCN2 0.91 (0.88–0.94) - Combined Asians [7]
rs3781913, rs79145843 11:72662452 PDE2A-ARAP1 0.88 (0.84–0.91) Yes Combined Asians, Trans Meta [7, 8, 50]
rs4409785 11:95578258 CEP57 0.91 (0.88–0.94) - Combined Europeans, Trans Meta [6, 7]
rs138193887 11:108096623 CUL5 1.21 (1.13–1.29) - Combined Europeans [6]
rs10892279, rs4938573, rs73005423 11:118741072 DDX6 1.15 (1.09–1.22) - Positive Asians, Europeans [8, 46, 50]
rs10790268 11:118858682 CXCR5 0.87 (0.84–0.90) Yes Combined Europeans [6]
rs12795702 11:128286419 LOC107984408 1.09 (1.06–1.12) - Combined Trans Meta [7]
rs73013527, rs10556591 11:128627057 FLI1-ETS1 0.92 (0.90–0.95) Yes Combined Trans Meta [6, 8]
rs4963581 12:24660347 LOC105369698 1.09 (1.06–1.12) - Combined Trans Meta [7]
rs1427749 12:45976333 SCAF11 1.08 (1.05–1.11) Yes Combined Trans Meta [8]
rs773125, rs4622308, rs705700 12:56001170 CDK2 1.09 (1.07–1.12) Yes Combined Europeans, Trans Meta [6, 7]
rs10683701, rs1696466 12:57698305 OS9-AGAP2 1.06 (1.04–1.08) - Positive Europeans, Trans Meta [8, 46]
rs10774624, rs77465633, rs3184504 12:111395984 SH2B3-PTPN11 1.32 (1.20–1.45) Yes Combined Asians, Europeans [6, 7]
rs61944750 13:28060796 FLT3 0.91 (0.88–0.94) Yes Combined Trans Meta [8]
rs9603616, rs9532434 13:39793932 COG6 0.89 (0.87–0.91) - Combined Asians, Europeans [6, 7]
rs2147161 13:42408166 AKAP11-LINC02341 1.10 (1.06–1.13) - Positive Europeans [8]
rs9557321 13:99868847 CLYBL 1.73 (1.42–2.11)* - Negative Europeans [34]
rs3783782, rs146492555 14:61473957 PRKCH 1.14 (1.09–1.18) - Combined Asians, Trans Meta [6, 8]
rs1950897, rs1885013 14:68293424 RAD51B 1.11 (1.08–1.14) - Combined Asians, Europeans [6, 7]
rs3825568 14:68793871 ZFP36L1 1.08 (1.06–1.11) - Combined Asians, Trans Meta [7, 48]
rs175714 14:75515513 BATF 0.94 (0.92–0.96) Yes Combined Trans Meta [8]
rs2841277, rs2582532, rs3001423 14:104924668 PLD4 0.85 (0.82–0.88) - Combined Asians [6, 8, 50]
rs8043085, rs8032939, rs6495979 15:38535939 RASGRP1 0.88 (0.86–0.90) Yes Positive Asians, Europeans [68, 46]
rs8026898 15:69699078 TLE3 1.14 (1.11–1.17) Yes Combined Europeans, Trans Meta [8, 46]
rs115284761 15:77034495 PSTPIP1 0.91 (0.89–0.94) Yes Combined Europeans, Trans Meta [8]
rs199894206, rs7171617 15:90495653 IQGAP1 1.12 (1.08–1.16) - Combined Asians, Trans Meta [7, 8]
rs4780401, rs7206670, rs4584833 16:11745470 TXNDC11 1.07 (1.05–1.10) - Combined Europeans, Trans Meta [6, 7]
rs149041927 16:23859897 PRKCB 0.91 (0.88–0.94) Yes Combined Asians [7]
rs12918327, rs34480360 16:30615295 ZNF689 1.09 (1.06–1.12) - Combined Trans Meta [7, 8]
rs13330176, rs9927316 16:85985481 IRF8 0.91 (0.89–0.94) Yes Positive Asians, Europeans [68, 46]
rs72634030, rs8073171 17:5369285 C1QBP 1.12 (1.08–1.17) Yes Combined Trans Meta [6, 8]
rs11375064 17:27577049 KSR1 0.93 (0.90–0.95) - Positive Trans Meta [8]
rs1877030 17:39583908 MED1 1.09 (1.06–1.12) - Combined Trans Meta [6]
rs2305480, rs2872507, rs56750287 17:39905943 GSDMB 0.93 (0.91–0.95) Yes Combined Europeans, Trans Meta [6, 8, 46]
rs591549 18:3542249 DLGAP1 0.91 (0.88–0.94) - Combined Trans Meta [8]
rs2847297, rs8083786, rs7241016 18:12797695 PTPN2 0.91 (0.89–0.94) Yes Combined Asians, Europeans [6, 8, 50]
rs866205108 18:62342401 TNFRSF11A 1.10 (1.06–1.14) Yes Positive Trans Meta [8]
rs2469434, rs143107126 18:69876810 CD226 1.07 (1.05–1.10) Yes Combined Asians, Trans Meta [6, 8]
rs1943199 18:75750899 LINC01898 1.94 (1.54–2.44)* - Negative Europeans [34]
rs10415976 19:941603 ARID3A 0.92 (0.90–0.95) - Combined Trans Meta [8]
rs34536443 19:10352442 TYK2 0.68 (0.62–0.75) Yes Positive Europeans [46]
rs147622113 19:10661265 ILF3 0.68 (0.60–0.77) Yes Combined Europeans [6]
rs55762233 19:19256510 HAPLN4 1.10 (1.07–1.14) - Combined Trans Meta [8]
rs28373672 19:35722170 KMT2B 0.93 (0.91–0.96) - Combined Trans Meta [8]
rs8106598 19:51514686 SIGLEC6 1.08 (1.05–1.11) - Positive Trans Meta [8]
rs6032662, rs4810485, rs1883832 20:46105671 CD40 0.90 (0.88–0.92) Yes Positive Asians, Europeans [6, 8, 46, 51]
rs6011186, rs4809371 20:63852655 C20orf181 0.90 (0.87–0.93) - Combined Asians, Trans Meta [7, 8]
rs73194058, rs8126756, rs2300373 21:33391982 IFNGR2 1.09 (1.06–1.12) Yes Combined Europeans, Trans Meta [68]
rs9979383, rs8133843, rs66922517 21:35343463 RUNX1 1.08 (1.06–1.11) Yes Combined Europeans, Trans Meta [68, 46]
rs1893592 21:42434957 UBASH3A 1.10 (1.07–1.13) Yes Combined Europeans, Trans Meta [6]
rs2075876, rs7278257, rs11454989 21:44289270 AIRE 0.91 (0.89–0.94) Yes Combined Asians, Trans Meta [7, 8, 54]
rs11089637, rs5754104 22:21624807 UBE2L3-YDJC 1.09 (1.06–1.12) Yes Combined Europeans, Trans Meta [68]
rs5756407 22:36920217 CSF2RB-LOC105373023 1.06 (1.04–1.08) Yes Combined Trans Meta [8]
rs909685, rs2069235 22:39351666 SYNGR1 1.14 (1.11–1.17) - Combined Asians, Europeans [6, 7]
rs35156883 22:45350272 SMC1B 1.10 (1.06–1.13) - Combined Asians [7]
rs201408742, rs6619397, rs74842123 X:79209119 GPR174-KIF4CP 1.11 (1.08–1.15) Yes Combined Asians, Trans Meta [68]
rs13397, rs5987194 X:153982797 IRAK1 1.15 (1.12–1.18) Yes Positive Asians, Europeans [6, 7, 46]

1Genetic variation with genome-wide significance for association

2Position is indicated for the first variation in the list

3Trans Meta – meta-analysis for populations with European and Asian ancestry

OR odds ratio, 95%CI 95% confidence interval for OR, ACPA anti-citrullinated peptide/protein antibodies