openSNP | rs3197999

Links to SNPedia

Title	Summary
rs3197999 T/T	1.2x risk of crohn's

Note: For some SNPs, testing providers detect the genotype from the opposite strand of DNA, so that the genotypes listed on openSNP don't appear here. In those cases, please replace "A" by "T" or "G" by "C" (and vice-versa).

Publications on this SNP on the Public Library of Science:

First Author	Title	Year of Publication	# of readers
Steven E. Kauder	Functional Consequences of the Macrophage Stimulating Protein 689C Inflammatory Bowel Disease Risk Allele	2013	3297
Alexandra C. Nica	Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations	2010	15578
Karin Fransen	Limited Evidence for Parent-of-Origin Effects in Inflammatory Bowel Disease Associated Loci	2012	2553
Natalia Gorlatova	Protein Characterization of a Candidate Mechanism SNP for Crohn's Disease: The Macrophage Stimulating Protein R689C Substitution	2011	3277
Garima Juyal	An Investigation of Genome-Wide Studies Reported Susceptibility Loci for Ulcerative Colitis Shows Limited Replication in North Indians	2011	4399
Camille Jung	Genotype/Phenotype Analyses for 53 Crohn’s Disease Associated Genetic Polymorphisms	2012	4139
Elizabeth J. Rossin	Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology	2011	30827
Christoph Preuss	Evolutionary Dynamics of Co-Segregating Gene Clusters Associated with Complex Diseases	2012	2677
Antonio F. Di Narzo	High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors	2017	4477
Orazio Palmieri	Crohn’s Disease Localization Displays Different Predisposing Genetic Variants	2017	1725
Wei-Qi Wei	Evaluating phecodes, clinical classification software, and ICD-9-CM codes for phenome-wide association studies in the electronic health record	2017	2131
Sofie Haglund	Combination treatment with 6-mercaptopurine and allopurinol in HepG2 and HEK293 cells – Effects on gene expression levels and thiopurine metabolism	2017	1976

Publications on this SNP on Mendeley

First Author	Title	Pub. Year	# of Readers	DOI
Roger Chapman	Genome-wide association studies in primary sclerosing cholangitis: still more questions than answers?	2011	1	10.1002/hep.24333
T H Karlsen	Genome-wide association analysis in primary sclerosing cholangitis	2010	4	S0016-5085(09)02063-0 [pii]\r10.1053/j.gastro.2009.11.046
M Krawczyk	Macrophage stimulating protein variation enhances the risk of sporadic extrahepatic cholangiocarcinoma.	2013	1	10.1016/j.dld.2012.12.017
E Melum	Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci	2011	3	ng.728 [pii]\r10.1038/ng.728
T H Karlsen	Genome-wide association analysis in primary sclerosing cholangitis	2010	8	10.1053/j.gastro.2009.11.046
UK-PSC Consortium	Fine mapping and replication of genetic risk loci in primary sclerosing cholangitis	2012	3	10.3109/00365521.2012.682090
Espen Melum	Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci.	2011	22	-
Roger Chapman	Genome-wide association studies in primary sclerosing cholangitis: still more questions than answers?	2011	0	10.1002/hep.24333
D Berard	Macrophage-stimulating protein polymorphism rs3197999 is associated with a gain of function: implications for inflammatory bowel disease	2012	2	10.1038/gene.2011.88
P Goyette	Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis.	2008	21	-
P Goyette	Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis.	2008	25	10.1038/mi.2007.15
Espen Melum	Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci.	2011	3	10.1038/ng.728
Espen Melum	Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci.	2011	9	10.1038/ng.728
Brijesh Srivastava	Fine mapping and replication of genetic risk loci in primary sclerosing cholangitis.	2012	2	10.3109/00365521.2012.682090
Tom H Karlsen	Genome-wide association analysis in primary sclerosing cholangitis.	2010	16	10.1053/j.gastro.2009.11.046
F Hauser	Macrophage-stimulating protein polymorphism rs3197999 is associated with a gain of function: implications for inflammatory bowel disease	2012	0	10.1038/gene.2011.88
P Goyette	Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis	2008	1	-
Marcin Krawczyk	Macrophage stimulating protein variation enhances the risk of sporadic extrahepatic cholangiocarcinoma	2013	2	10.1016/j.dld.2012.12.017
E Melum	Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci	2011	4	ng.728 [pii]\r10.1038/ng.728
M Krawczyk	Macrophage stimulating protein variation enhances the risk of sporadic extrahepatic cholangiocarcinoma.	2013	1	10.1016/j.dld.2012.12.017

Evidence compiled by the Personal Genome Project

There are no results from the Personal Genome Project yet. Please come back later.

Publications listed by Genome.gov

First Author	Title	Journal	Publication Date	Trait	p-value	Confidence Interval
Franke A	Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.	Nat Genet	11/21/2010	Crohn's disease	6.0e-17	[1.16-1.27]
Barrett JC	Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.	Nat Genet	06/29/2008	Crohn's disease	1.0e-12	[NR]
McGovern DP	Genome-wide association identifies multiple ulcerative colitis susceptibility loci.	Nat Genet	03/14/2010	Ulcerative colitis	4.0e-09	[NR]
Melum E	Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci.	Nat Genet	12/12/2010	Primary sclerosing cholangitis	1.0e-16	[1.24-1.56]

Name	rs3197999
Chromosome	3
Position	49684099
Weight of evidence	57

	AG
	GG
	AA
	CT

SNP rs3197999

Basic Information

Genotype Frequency

Allele Frequency

Additional Information

Links to SNPedia

Publications on this SNP on the Public Library of Science:

Publications on this SNP on Mendeley

Evidence compiled by the Personal Genome Project

Publications listed by Genome.gov

Users who share this SNP:

Genome Browser

Contacts

SNP rs3197999

Basic Information

Genotype Frequency

Allele Frequency

Additional Information

Links to SNPedia

Publications on this SNP on the Public Library of Science:

Publications on this SNP on Mendeley

Evidence compiled by the Personal Genome Project

Publications listed by Genome.gov

Users who share this SNP:

Genome Browser

Human GrCh38/hg38

Contacts