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Genes and mutations associated with autoimmune diseases

If you tested your DNA with a personal genomics service like 23andMe, DeCODEme, FTDNA's Family Finder or another testing company, you can learn more about your risk factors for hundreds of diseases. Many of these SNP's are tested but not (yet) part of the report provided by personal genomics companies. This is free extra information.

We recommend that you install the SNPTips add-on for Mozilla Firefox to browse these pages. It allows you to upload your DNA results in the browser and show instantly which allele variant you have for each of the SNP listed below.

What can DNA tell you about yourself ?

List of auto-immune diseases with the associated genes

Risk alleles : Substantially lower risk (over 3x less), moderately lower risk (up to 3x less), normal, slightly higher risk (up to 3x more), greatly increased risk (over 3x more). Normal alleles marked with a * mean that the person is a carrier of the disease. Depending on the testing company, sometimes A is reported as T, and G is reported as C, or vice-versa. Question marks (?) mean that we doubt the validity of the risk alleles because they are too common.

Testing companies :
A = 23andMe
(all versions) ; A2* = 23andMe (v2 only) ; A2 = 23andMe (v2 & v3) ; A3 = 23andMe (v3 only)
B = DeCODEme
Bold letters indicate that the SNP is part of the official report, and is therefore likely to be more reliable. Only SNP's in the official report are listed for deCODEme.

Description Chromosome Gene SNP Risk alleles Tested by*
Allergies (general) A FCER1A rs2427837 AA, AG, GG A3
rs2251746 CC, CT, TT A
Ankylosing Spondylitis 5 ARTS-1 rs27044 CC, CG, GG A
rs17482078 CC, CT, TT A3
rs10050860 CC, CT, TT A
rs30187 CC, CT, TT A
rs2287987 CC, CT, TT A3
A IL23R rs11209026 AA, AG, GG A
rs1004819 CC, CT, TT A
rs10489629 AA, AG, GG A2*
rs11465804 GG, GT, TT A
rs1343151 CC, CT, TT A
rs10889677 AA, AC, CC A
5 LNPEP rs2303138 AA, AG, GG A
6 - rs7743761 AA, AC, CC A
12 CLSTN3 rs7302230 AA, AG, GG A
Asthma A intergenic rs4950928 CC, CG, GG A
6 PLA2G7 rs1805018 A, B
rs1051931 A, B
6 TNF rs1800629 AA, AG, GG A
7 AAA1 rs324981 A
11 GSTP1 rs1695 AA, AG, GG A, B
17 GSDML rs7216389 CC, CT, TT A, B
Celiac Disease A RGS1 rs2816316 A, B
B intergenic rs917997 CC, CT, TT A, B
3 intergenic rs6441961 A, B
3 intergenic rs17810546 AA, AG, GG A, B
3 LPP rs1464510 A, B
4 KIAA1109 rs13119723 A
4 intergenic rs6822844 GG, GT, TT A, B
6 HLA-DQA1 rs2187668 CC, CT, TT A, B
6 TAGAP rs1738074 AA, AG, GG A, B
12 SH2B3 rs3184504 CC, CT, TT A, B
19 MYO9B rs2305764 AA, AG, GG A
rs2305767 CC, CT, TT A
Crohn's Disease A IL23R rs11209026 AA, AG, GG A, B
rs11805303 CC, CT, TT A
B ATG16L1 rs2241880 AA, AG, GG A, B
rs10210302 CC, CT, TT A
3 BSN rs9858542 AA, AG, GG A, B
3 MST rs3197999 AA, AG, GG A
5 5p13 region rs17234657 GG, GT, TT A, B
5 IBD5 rs12521868 A, B
5 IRGM rs4958847 AA, AG, GG A, B
rs7714584 AA, AG, GG A
6 TNF rs1800629 AA, AG, GG A
7 ABCB1 rs3789243 A
10 NKX2-3 rs11190140 CC, CT, TT A, B
10 intergenic rs10761659 AA, AG, GG A
10 intergenic rs224136 CC, CT, TT A, B
11 NELL1 rs1519717 A, B
rs1793000 A, B
16 NOD2(1) rs2066844 CC, CT, TT A
16 NOD2(2) rs2066845 CC, CG, GG A
rs2066843 A, B
16 NOD3(3) rs2066847 A
18 PTPN2 rs1893217 AA, AG, GG A
rs2542151 GG, GT, TT A, B
22 XBP1 rs35873774 A3
Type-1 Diabetes A PTPN22 rs2476601 A
rs6679677 A, B
B CTLA4 rs3087243 A
rs11571316 A
rs231804 A, B
B IFIH1 rs1990760 A, B
4 intergenic rs6822844 A, B
6 HLA rs3129934 A, B
rs9272346 A
10 IL2RA rs2104286 A, B
11 INS rs3741208 A, B
12 SH2B3 rs3184504 A
12 C12orf30 rs17696736 A, B
12 ERBB3 rs2292239 A, B
16 KIAA0350 rs725613 A, B
18 PTPN2 rs1893217 A
rs2542151 A, B
Type-2 Diabetes A NOTCH2 rs2793831 A, B
B THADA rs7578597 A, B
3 PPARG rs1801282 A, B
rs6802898 A
rs2197423 A
3 IGF2BP2 rs4402960 A, B
4 WFS1 rs10012946 A
5 ADRB2 rs1042714 A
6 CDKAL1 rs4712523 A
rs7756992 A, B
7 JAZF1 rs1635852 A, B
8 SLC30A8 rs13266634 A, B
9 CDKN2A/B rs2383208 A, B
9 intergenic rs10811661 CC, CT, TT A
10 TCF7L2 rs7903146 A, B
rs7901695 A
10 HHEX rs1111875 A, B
rs5015480 A
11 KCNJ11 rs5219 A
rs5215 A, B
12 intergenic rs1353362 A, B
Graves' disease A FCRL3 rs7528684 A
A IL23R rs10889677 A
rs2201841 A
rs7530511 A
A RSBN1 rs3789604 A
B CTLA4 rs231775 A
rs733618 A2*
6 ITPR3 rs3748079 A
6 TNF rs1799964 A
rs1800630 A
rs1800629 AA, AG, GG A
Inflammatory bowel disease B IL1B rs1143634 CC, CT, TT A
Multiple Sclerosis A RPL5 rs6604026 CC, CT, TT A
A CD58 rs12044852 AA, AC, CC A
A FAM69A rs7536563 AA, AG, GG A
rs11164838 CC, CT, TT A
A EVI5 rs10735781 CC, CG, GG A
rs6680578 AA, AT, TT A
A PDE4B rs1321172 CC, CG, GG A
B ALK rs7577363 AA, AG, GG A
3 CBLB rs12487066 CC, CT, TT A
5 IL7RA rs6897932 CC, CT, TT A, B
6 HLA-DRB1 rs3135388 AA, AG, GG A, B
7 IRF5 rs3807306 A
7 intergenic rs4728142 A
9 DBC1 rs10984447 AA, AG, GG A
9 ANKRD1 rs10975200 AA, AG, GG A
10 IL2RA rs12722561 CC, CT, TT A, B
rs12722489 AA, AG, GG A
rs2104286 AA, AG, GG A
12 LAG3 rs870849 A
12 KLRB1 rs4763655 AA, AG, GG A3
14 KLC1 rs8702 CC, CG, GG A3
16 KIAA0350 rs6498169 AA, AG, GG A
Psoriasis A IL23R rs11209026 AA, AG, GG A, B
rs2201841 AA, AG, GG A
A intergenic rs4112788 AA, AG, GG A
A intergenic rs4085613 GG, GT, TT A
5 IL12B rs3212227 GG, GT, TT A, B
rs3213094 CC, CT, TT A
5 IL13 rs20541 AA, AG, GG A
6 PSORS1C3 rs887466 A
6 HLA-Cw0602 rs1265181 CC, CG, GG A3
6 HLA-C rs1265159 AA, AG, GG A
6 HLA-C rs10484554 CC, CT, TT A, B
6 TNF rs361525 AA, AG, GG A
6 TNFAIP3 rs610604 GG, GT, TT A
12 STAT2 rs2066808 AA, AG, GG A
Rheumatoid Arthritis A PTPN22 rs2476601 AA, AG, GG A, B
A PADI4 rs11203366 AA, AG, GG A
rs2240340 AA, AG, GG A
A MMEL1 rs3890745 CC, CT, TT A
rs6684865 AA, AG, GG A
A FCRL3 rs7528684 AA, AG, GG A
A RSBN1 rs6679677 A
A intergenic rs11162922 A
B STAT4 rs7574865 A, B
B CTLA4 rs3087243 A
B ITGAV rs3738919 A
4 intergenic rs6822844 A, B
4 ANAPC4 rs3816587 A
6 HLA-DRB1 rs6457617 CC, CT, TT A, B
6 6q23 rs2327832 AA, AG, GG A, B
rs13192841 A, B
6 intergenic rs6920220 A
7 IRF5 rs2004640 A2*
7 intergenic rs11761231 A
9 TRAF1/C5 rs3761847 AA, AG, GG A, B
9 intergenic rs10818488 A
9 PHF19 rs1953126 A
10 IL2RA rs2104286 A
13 intergenic rs9550642 A
21 intergenic rs2837960 A
22 intergenic rs743777 A
Sjögren's Syndrome B STAT4 rs7574865 GG, GT, TT A
Systemic Lupus Erythematosis (Lupus) B STAT4 rs7574865 GG, GT, TT A
6 HLA-DQA1 rs2187668 CC, CT, TT A
6 TNF rs1800629 AA, AG, GG A
7 IRF5 rs10488631 CC, CT, TT A
16 ITGAM rs9888739 CC, CT, TT A
Ulcerative colitis A ECM1
A RUNX3 rs2236851
B IL1B rs1143634 CC, CT, TT A
B IL1RN rs423904 A3
5 PTPRS
7 ABCB1 rs3789243 A
7 MDR1
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