{{Rsnum
|rsid=2241879
|Gene=ATG16L1
|Chromosome=2
|position=233274822
|Orientation=minus
|GMAF=0.3889
|Gene_s=ATG16L1,SCARNA5
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(C;C)
|geno2=(C;T)
|geno3=(T;T)
}}{{ population diversity
| geno1=(C;C)
| geno2=(C;T)
| geno3=(T;T)
| CEU | 14.3 | 55.4 | 30.4
| HCB | 41.8 | 44.0 | 14.2
| JPT | 59.3 | 37.2 | 3.5
| YRI | 55.8 | 36.7 | 7.5
| ASW | 53.6 | 41.1 | 5.4
| CHB | 41.8 | 44.0 | 14.2
| CHD | 57.8 | 36.7 | 5.5
| GIH | 27.7 | 48.5 | 23.8
| LWK | 61.5 | 31.2 | 7.3
| MEX | 53.6 | 32.1 | 14.3
| MKK | 50.0 | 46.2 | 3.8
| TSI | 14.7 | 60.8 | 24.5
| HapMapRevision=28
}}

[[rs2241879]] has been associated with [[Crohn's disease]]; the minor allele is somewhat protective in that it lessens the odds of acquiring the disease (odds ratio 0.74, CI: 0.65-0.84, p=3.6x10e-6).{{PMID|18162085}}

{{ neighbor
| rsid = 2241880
| distance = 100
}}

{{PMID Auto
|PMID=21206965
|Title=IL23R, NOD2/CARD15, ATG16L1 and PHOX2B polymorphisms in a group of patients with Crohn's disease and correlation with sub-phenotypes
}}

{{PMID Auto
|PMID=21513755
|Title=ATG16L1 gene polymorphisms are associated with palmoplantar pustulosis
}}

{{PMID Auto
|PMID=18698678
|Title=Replication of interleukin 23 receptor and autophagy-related 16-like 1 association in adult- and pediatric-onset inflammatory bowel disease in Italy.
|OA=1
}}

{{PMID Auto
|PMID=19916168
|Title=Genome-wide association studies--a summary for the clinical gastroenterologist.
|OA=1
}}

{{PMID Auto
|PMID=20066736
|Title=Interaction of the major inflammatory bowel disease susceptibility alleles in Crohn's disease patients.
|OA=1
}}

{{PMID Auto
|PMID=20082483
|Title=NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease.
|OA=1
}}

{{PMID Auto
|PMID=20195480
|Title=The cannabinoid 1 receptor (CNR1) 1359 G/A polymorphism modulates susceptibility to ulcerative colitis and the phenotype in Crohn's disease.
|OA=1
}}

{{PMID Auto
|PMID=20222171
|Title=T300A polymorphism of ATG16L1 and susceptibility to inflammatory bowel diseases: a meta-analysis.
|OA=1
}}

{{PMID Auto
|PMID=20380008
|Title=NOD2/CARD15, ATG16L1 and IL23R gene polymorphisms and childhood-onset of Crohn's disease.
|OA=1
}}

{{PMID Auto
|PMID=20454450
|Title=Evidence for STAT4 as a common autoimmune gene: rs7574865 is associated with colonic Crohn's disease and early disease onset.
|OA=1
}}

{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | FTDNA2}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}