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rs3197999

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(T;T) 2 1.2x risk of Crohn's
Make rs3197999(C;C)
Make rs3197999(C;T)
ReferenceGRCh38 38.1/141
Chromosome3
Position49684099
GeneMST1
is asnp
is mentioned by
dbSNPrs3197999
ebirs3197999
HLIrs3197999
Exacrs3197999
Varsomers3197999
Maprs3197999
PheGenIrs3197999
hapmaprs3197999
1000 genomesrs3197999
hgdprs3197999
ensemblrs3197999
gopubmedrs3197999
geneviewrs3197999
scholarrs3197999
googlers3197999
pharmgkbrs3197999
gwascentralrs3197999
openSNPrs3197999
23andMers3197999
23andMe allrs3197999
SNP Nexus

SNPshotrs3197999
SNPdbers3197999
MSV3drs3197999
GWAS Ctlgrs3197999
GMAF0.2153
Max Magnitude2
? (C;C) (C;T) (T;T) 28
via spitoon reports about 10.1038/ng.175 which identifies 32 snps relevant to Crohn's disease: Out of a possible total of 46, 80% of people will have between 17 and 25 copies of the riskier versions of these SNPs. Because there are so many of these SNPs--and because the riskier versions are often more common than their less risky counterparts--even people at the high end of the distribution are not much more likely than average to develop Crohn's disease.

Proxy snps on 23andMe

GWAS snp
PMID [PMID 18587394OA-icon.png]
Trait Crohn's disease
Title Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease
Risk Allele A
P-val 9.9999999999999998E-13
Odds Ratio 1.20 [NR]
OMIM612241
DescINFLAMMATORY BOWEL DISEASE 12; IBD12
Variant
Relatedalso


[PMID 20024904] Variants at the 3p21 locus influence susceptibility and phenotype both in adults and early-onset patients with inflammatory bowel disease


[PMID 19944697] Genome-wide association analysis in primary sclerosing cholangitis

GWAS snp
PMID [PMID 20228799OA-icon.png]
Trait Ulcerative colitis
Title Genome-wide association identifies multiple ulcerative colitis susceptibility loci
Risk Allele T
P-val 4E-9
Odds Ratio 1.20 [NR]
GWAS snp
PMID [PMID 21151127OA-icon.png]
Trait
Title Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci
Risk Allele
P-val 1E-16
Odds Ratio 1.3900 [1.24-1.56]
GWAS snp
PMID [PMID 21102463OA-icon.png]
Trait
Title Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
Risk Allele A
P-val 6E-17
Odds Ratio 1.2200 [1.16-1.27]


[PMID 18438406OA-icon.png] Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.


[PMID 19079170OA-icon.png] Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis.


[PMID 19474294OA-icon.png] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.


[PMID 20018022OA-icon.png] Replication of recently identified associated single-nucleotide polymorphisms from six autoimmune diseases in Genetic Analysis Workshop 16 rheumatoid arthritis data.


[PMID 20369022OA-icon.png] Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.


[PMID 21304977OA-icon.png] An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians.


[PMID 22237417] Macrophage-stimulating protein polymorphism rs3197999 is associated with a gain of function: implications for inflammatory bowel disease.


[PMID 22554193] Fine mapping and replication of genetic risk loci in primary sclerosing cholangitis.


GET Evidence
MST1-R689C
aa_change Arg689Cys
aa_change_short R689C
impact not reviewed
qualified_impact Insufficiently evaluated not reviewed
overall_frequency 0.122222
summary



GWAS snp
PMID [PMID 23128233OA-icon.png]
Trait Inflammatory bowel disease
Title Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Risk Allele A
P-val 1E-47
Odds Ratio 1.18 [1.144-1.216]


[PMID 23422030] Macrophage stimulating protein variation enhances the risk of sporadic extrahepatic cholangiocarcinoma.