{{Rsnum
|rsid=9858542
|Gene=BSN
|Chromosome=3
|position=49664550
|Orientation=plus
|ReferenceAllele=G
|GMAF=0.2199
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(A;A)
|geno2=(A;G)
|geno3=(G;G)
|Gene_s=BSN
}}{{ population diversity
| geno1=(A;A)
| geno2=(A;G)
| geno3=(G;G)
| CEU | 4.4 | 42.5 | 53.1
| HCB | 0.0 | 8.9 | 91.1
| JPT | 0.0 | 8.8 | 91.2
| YRI | 8.2 | 28.6 | 63.3
| ASW | 1.8 | 49.1 | 49.1
| CHB | 0.0 | 8.9 | 91.1
| CHD | 1.8 | 10.1 | 88.1
| GIH | 5.0 | 35.6 | 59.4
| LWK | 10.2 | 37.0 | 52.8
| MEX | 3.4 | 39.7 | 56.9
| MKK | 8.3 | 35.9 | 55.8
| TSI | 7.8 | 52.0 | 40.2
| HapMapRevision=28
}}[[rs9858542]] has been reported in a large study to be associated with [[Crohn's disease]].

The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.09 (CI 0.96-1.24), and for homozygotes, 1.84 (CI 1.49-2.26). {{PMID|17554300|OA=1
}}

{{GWAS Summary
|SNP=rs9858542
|PubMedID=17554261
|Condition=Crohn's disease
|Gene=MST1
|Risk Allele=
|pValue=5.00E-008
|OR=1.17
|95CI=1.14-1.31
|OA=1
}}

{{omim
|desc=INFLAMMATORY BOWEL DISEASE 12; IBD12
|id=612241
|rsnum=9858542
}}

{{PharmGKB
|RSID=rs9858542
|Name_s=
|Gene_s=BSN, APEH
|Feature=
|Evidence=PubMed ID:17554261; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS results: Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: 1,182 cases, 2,024 controls). This variant is associated with Crohn's disease.
|Drugs=
|Drug Classes=
|Diseases=Crohn Disease
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA162356572
}}
{{PMID Auto
|PMID=20024904
|Title=Variants at the 3p21 locus influence susceptibility and phenotype both in adults and early-onset patients with inflammatory bowel disease
}}
{{PMID Auto GWAS
|PMID=19915572
|Trait=Ulcerative colitis
|Title=Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region
|RiskAllele=
|Pval=7E-9
|OR=NR
|ORtxt=NR
|OA=1
}}
{{PMID Auto
|PMID=19657358
|Title=Effect of BSN-MST1 locus on inflammatory bowel disease and multiple sclerosis susceptibility
}}

{{PharmGKB
|RSID=rs9858542
|Name_s=
|Gene_s=BSN, APEH
|Feature=
|Evidence=PubMed ID:17554300; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS Results: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Initial Sample Size: 1,748 cases, 2,938 controls; Replication Sample Size: (see Parkes 2007); Risk Allele: rs9858542-A). This variant is associated with crohn's disease.
|Drugs=
|Drug Classes=
|Diseases=Crohn Disease
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA162356661
}}

{{PMID Auto
|PMID=18224312
|Title=Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment.
|OA=1
}}

{{PMID Auto
|PMID=18438406
|Title=Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.
|OA=1
}}

{{PMID Auto
|PMID=18533027
|Title=Worldwide population differentiation at disease-associated SNPs.
|OA=1
}}

{{PMID Auto
|PMID=18853133
|Title=Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.
|OA=1
}}

{{PMID Auto
|PMID=19140132
|Title=Unbiased estimation of odds ratios: combining genomewide association scans with replication studies.
|OA=1
}}

{{PMID Auto
|PMID=20369022
|Title=Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.
|OA=1
}}

{{GET Evidence
|impact=pathogenic
|qualified_impact=Insufficiently evaluated pathogenic
|inheritance=unknown
|quality_scores=Array
|dbsnp_id=rs9858542
|overall_frequency_n=3013
|overall_frequency_d=10758
|overall_frequency=0.280071
|n_genomes=25
|n_genomes_annotated=0
|n_haplomes=31
|n_articles=0
|n_articles_annotated=0
|in_gwas=Y
|in_pharmgkb=Y
|autoscore=2
|webscore=N
}}

{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | Affy GenomeWide 6}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}