Crohn's disease

89 SNPs linked to Crohn's disease across 35 genes, 27 with a genotype of magnitude 2 or higher.

Type: Condition
SNPs: 89
Notable: 27Magnitude 2 or higher
Well documented: 64
Genes: 35

Linked SNPs

Every genotype, as shown in 23andMe and AncestryDNA files.

rs2066845NOD2Very important
- C;C~35x higher risk for Crohn's diseaseBad
- C;G3x higher risk for Crohn's diseaseBad
- G;Gcommon in complete genomicsGood
rs7574865STAT4Important
- G;Gnormal risk of rheumatoid arthritis, SLE, Sjögren's syndrome, type-1 diabetes, and primary biliary cirrhosis.Good
- G;T1.3x risk of rheumatoid arthritis; 1.55x risk of SLE; 1.42x risk of Sjögren's syndrome; increased risk of type-1 diabetes; and increased risk of primary biliary cirrhosis.Bad
- T;T1.69x risk of rheumatoid arthritis; 2.4x risk of SLE; 2.28x risk of Sjögren's syndrome; increased risk of type-1 diabetes; and increased risk of primary biliary cirrhosis.Bad
rs2066844NOD2Important
- C;Ccommon in complete genomicsGood
- C;TSignificance is unclear, but possibly, ~2x higher risk for Crohn's diseaseBad
- T;TSignificance unclear; possibly higher risk for Crohn's diseaseBad
rs6679677RSBN1Important
- A;A5.2x risk for T1D; 3.3x for RABad
- A;C1.8x risk for T1D; 2x risk for RABad
- C;CnormalGood
rs11209026IL23RImportant
- A;A0.26x lower risk for certain autoimmune diseases.Good
- A;G0.26x lower risk for certain autoimmune diseases.Good
- G;GNormal, but higher risk for certain autoimmune diseases.Bad
rs4958847IRGMWorth knowing
- A;A2.6x increased risk for Crohn's diseaseBad
- A;G1.3x increased risk for Crohn's diseaseBad
- G;GnormalGood
rs13361189Worth knowing
- C;C2.6x increased risk for Crohn's diseaseBad
- C;T1.3x increased risk for Crohn's diseaseBad
- T;TnormalGood
rs1800629TNFWorth knowing
- A;Acomplex; generally higher risk for certain diseasesBad
- A;Gcomplex; generally higher risk for certain diseasesBad
- G;Gcomplex; generally normal riskGood
rs2241880ATG16L1Worth knowing
- G;G2x-3x increased risk for Crohn's disease in CaucasiansBad
- A;G1.4x increased risk for Crohn's disease in CaucasiansBad
- A;AnormalGood
rs1050152SLC22A4Worth knowing
- C;CnormalGood
- C;T2.1x increased risk of Crohn's diseaseBad
- T;T2.1x increased risk of Crohn's diseaseBad
rs2301436FGFR1OPWorth knowing
- T;TNo summary available.Bad
- C;CNo summary available.Good
rs1128535TRAIPWorth knowing
- T;TnormalBad
- C;T0.77x risk for Crohn's diseaseGood
- C;Creduced risk (0.77x) for Crohn's diseaseGood
rs1800795IL6Worth knowing
- C;Cless IL6; certain risks, see detailsBad
- C;Gcomplex; see detailsNot rated
- G;Gmore IL6; certain risks, see detailsBad
rs1800972DEFB1Worth knowing
- G;Gnormal riskBad
- C;Gnormal riskBad
- C;Creduced risk for Crohn's disease; reduced risk for maternal HIV transmissionGood
rs1893217PTPN2Worth knowing
- G;GSomewhat increased (~2x) risk for Crohn's diseaseBad
- A;GSlightly increased (1.4x) risk for Crohn's diseaseBad
- A;Acommon/normalGood
rs2201841IL23RWorth knowing
- T;TNo summary available.Not rated
- G;G1.5x increased risk for Crohn's diseaseBad
- A;G1.5x increased risk for Crohn's disease; 2x increased risk for Graves' diseaseBad
- A;A2.4x increased risk for Graves' diseaseBad
rs2542151PTPN2Worth knowing
- G;G2x risk for Crohn's; 1.6x for T1DBad
- G;T1.3x risk for Crohn's; 1.3x for T1DBad
- T;TnormalGood
rs3197999MST1Worth knowing
- A;A1.2x risk of Crohn'sBad
rs6601764Worth knowing
- C;C1.52x increased risk of developing Crohn's diseaseBad
- C;T1.16x increased risk of developing Crohn's diseaseBad
- T;TNormal risk of developing Crohn's diseaseGood
rs6908425CDKAL1Worth knowing
- C;C1.95x increased risk of developing Crohn's diseaseBad
- C;T1.63x increased risk of developing Crohn's diseaseBad
- T;TNormal risk of developing Crohn's diseaseGood
rs7076156ZNF365Worth knowing
- A;ANo summary available.Not rated
- G;GNo summary available.Not rated
rs7807268Worth knowing
- C;C1.4x risk for Crohn's diseaseBad
- C;G1.3x risk for Crohn's diseaseBad
- G;GnormalNot rated
rs10883365LINC01475Worth knowing
- A;ANormal risk of developing Crohn's diseaseGood
- A;G1.2x increased risk for developing Crohn's diseaseBad
- G;G1.62x increased risk for developing Crohn's diseaseBad
- T;TNo summary available.Not rated
rs10889677IL23RWorth knowing
- A;A1.5x increased risk for certain autoimmune diseasesBad
- A;C1.5x increased risk for certain autoimmune diseases; 2x increased risk for Graves diseaseBad
- C;CBaseline (average) risk for certain autoimmune diseases; however, 2.3x increased risk for Graves diseaseBad
rs12037606Worth knowing
- A;A1.52x risk of developing Crohn's diseaseBad
- A;G1.22x risk of developing Crohn's diseaseBad
- C;CNo summary available.Not rated
- G;GNormal risk of developing Crohn's diseaseGood
rs17221417NOD2Worth knowing
- C;CnormalNot rated
- C;G1.3x higher risk for Crohn's diseaseBad
- G;G1.9x higher risk for Crohn's diseaseBad
rs10210302ATG16L1Minor
- C;Ccommon/normalGood
- C;T1.2x increased risk for Crohn's diseaseBad
- T;T1.8x increased risk for Crohn's diseaseBad
rs33995883LRRK2Minor
- A;Acommon/normalGood
- A;GSlight (1.8x) increase in risk for Crohn's diseaseBad
rs2488457PTPN22Minor
- G;Gcommon/normalGood
- C;GSlightly increased (~1.5x) risk for certain autoimmune diseases in some populationsBad
- C;CSlightly increased (~1.7x) risk for certain autoimmune diseases in some populationsBad
rs33996649PTPN22Minor
- C;Ccommon in complete genomicsGood
- C;TSlightly lower (~0.8x) risk for rheumatoid arthritisGood
- T;TSlightly lower (~0.65x) risk for rheumatoid arthritisGood
rs2032582ABCB1Minor
- T;Trare genotype, on a triallelic snpGood
- C;Cnormal. better response to atorvastatin. greater severity of delusions in male schizophrenics.Bad
- A;A4x higher risk for lung cancerBad
rs3814570TCF7L2Minor
- C;CNormal risk of developing Crohn's diseaseGood
- C;T1.3x increased risk for Crohn's disease with ileal involvementBad
- T;T1.3x increased risk for Crohn's disease with ileal involvementBad
rs11465770IL23RMinor
- C;Cnormal Crohn's Disease riskNot rated
- C;Tpossibly lower risk of Crohn's Disease (OR=0.30)Not rated
- T;Tpossibly lower risk of Crohn's Disease (OR=0.30)Not rated
rs12212067FOXO3Minor
- G;GLower inflammatory responseNot rated
- G;TLower inflammatory responseNot rated
- T;TGreater inflammatory responseNot rated
rs9858542BSNMinor
- A;A1.8x risk of Crohn's diseaseBad
- A;G1.1x risk Crohn's DiseaseBad
- G;GnormalNot rated
rs11362DEFB1Minor
- C;TNo summary available.Not rated
rs1004819IL23RMinor
- G;G1.5x risk of Crohn's disease, 1.2 for developing ankylosing spondylitisBad
- A;G1.5x risk of Crohn's disease, 1.2 for developing ankylosing spondylitisBad
- A;AcommonNot rated
rs10761659Minor
- A;A1.5x risk of Crohn's diseaseBad
- A;G1.2x risk of Crohn's diseaseBad
- G;GnormalGood
rs5051AGTTypical
- C;Cnormal riskGood
- C;Tincreased risk for hypertensionNot rated
- T;Tincreased risk for hypertensionNot rated
rs272893SLC22A4Typical
- C;Tcommon in complete genomicsGood
rs396991FCGR3ATypical
- C;CnormalNot rated
- A;Ccomplex; generally greater risk for cancer progressionNot rated
- A;Acomplex; generally greater risk for cancer progressionGood
rs1000113IRGMTypical
- C;CnormalGood
- C;T1.5x risk of Crohn's diseaseBad
- T;T1.9x risk of Crohn's diseaseBad
rs1793004NELL1Typical
- G;Gincreased risk for Crohn's diseaseBad
- C;G?Not rated
- C;C0.89x decreased risk for Crohn's diseaseGood
rs1800471TGFB1Typical
- C;Ccommon in clinvarGood
rs1800871IL10Typical
- G;G0.5x decreased risk for endometriosisNot rated
- A;G0.5x decreased risk for endometriosisGood
- A;AnormalNot rated
rs1800925TH2LCRRTypical
- C;Ccommon/normalGood
rs1992660PTGER4Typical
- T;Tincreased risk for Crohn's diseaseBad
- C;T?Not rated
- C;C0.72x decreased risk for Crohn's diseaseGood
rs1992662PTGER4Typical
- G;Gincreased risk for Crohn's diseaseNot rated
- A;G?Not rated
- A;A0.76x decreased risk for Crohn's diseaseNot rated
rs2076756NOD2Typical
- A;AnormalNot rated
- A;G?Not rated
- G;G1.7x increased risk for Crohn's diseaseBad
rs2188962IBD5Typical
- C;Ccommon./normalGood
rs2305767MYO9BTypical
- T;Tcommon/normalGood
rs2631367LOC553103Typical
- G;GIncreased risk for Crohn's DiseaseBad
- C;GIncreased risk for Crohn's DiseaseBad
- C;CNormalGood
rs3792876SLC22A4Typical
- C;CNo summary available.Not rated
rs6596075IBD5Typical
- C;C2x risk of Crohn's diseaseBad
- C;G1.5x riskBad
- G;GnormalNot rated
rs7517847IL23RTypical
- G;G0.65x reduced risk for Crohn's diseaseGood
- G;Tpossibly reduced risk for Crohn's diseaseNot rated
- T;TnormalNot rated
rs7714584IRGMTypical
- A;Acommon in complete genomicsGood
rs7753394Typical
- C;C1.5x risk of Crohn's diseaseBad
- C;T1.2x risk of Crohn's diseaseBad
- T;TnormalNot rated
rs8111071RSPH6ATypical
- A;AnormalNot rated
- A;G1.5x riskNot rated
- G;G1.3x riskNot rated
rs9469220Typical
- A;A1.5x risk of Crohn's diseaseBad
- A;G1.1x risk of Crohn's diseaseBad
- C;CNo summary available.Not rated
- G;GnormalNot rated
rs10065172IRGMTypical
- C;Ccommon in complete genomicsGood
rs10130695PPM1ATypical
- C;CNo summary available.Not rated
rs11568506SLC22A4Typical
- G;Gcommon in complete genomicsGood
rs11805303IL23RTypical
- C;CnormalGood
- C;T1.4x risk of Crohn's diseaseBad
- T;T1.8x risk of Crohn's diseaseBad
rs17234657Typical
- A;ANo summary available.Not rated
- G;G2.3x riskNot rated
- G;T1.5x riskNot rated
- T;TnormalNot rated
rs2066847NOD2Very important
- -;-common in complete genomicsGood
- -;C3x higher risk of Crohn's diseaseBad
- C;C35x higher risk for Crohn's diseaseBad
- G;Gcommon on affy axiom dataGood

Other SNPs

No notable genotype or detailed notes

Show 24 SNPs

Source and license

Adapted from Crohn's disease on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.

SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.

Linked SNPs

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Genes

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Source and license