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rs6679677

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(A;A) 3 5.2x risk for T1D; 3.3x for RA
(A;C) 2.3 1.8x risk for T1D; 2x risk for RA
(C;C) 0 normal
ReferenceGRCh38 38.1/141
Chromosome1
Position113761186
GenePHTF1
is asnp
is mentioned by
dbSNPrs6679677
ebirs6679677
HLIrs6679677
Exacrs6679677
Varsomers6679677
Maprs6679677
PheGenIrs6679677
hapmaprs6679677
1000 genomesrs6679677
hgdprs6679677
ensemblrs6679677
gopubmedrs6679677
geneviewrs6679677
scholarrs6679677
googlers6679677
pharmgkbrs6679677
gwascentralrs6679677
openSNPrs6679677
23andMers6679677
23andMe allrs6679677
SNP Nexus

SNPshotrs6679677
SNPdbers6679677
MSV3drs6679677
GWAS Ctlgrs6679677
GMAF0.04132
Max Magnitude3
? (A;A) (A;C) (C;C) 28
rs6679677 has been reported in a large study to be associated with rheumatoid arthritis.

The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.98 (CI 1.72-2.27), and for homozygotes, 3.32 (CI 1.93-5.69). [PMID 17554300OA-icon.png]

rs6679677 was also reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.82 (CI 1.59-2.09), and for homozygotes, 5.19 (CI 3.15-8.55). [PMID 17554300OA-icon.png]

Recently (Feb 2008), it has been asserted that the association between rs6679677 and type-1 diabetes is actually completely due to a closely linked, potentially causal variant identified as rs2476601, which is also known as Arg620Trp. In this study, apparently the largest to date, the odds ratio for the risk allele (of rs6679677) was reported to be 1.88 (CI: 1.66-2.13).[PMID 18305142]

DeCode reports that the CC genotype is associated with 1.05x higher odds of Crohn's disease. [PMID 18587394OA-icon.png]

GWAS snp
PMID [PMID 18978792OA-icon.png]
Trait Type 1 diabetes
Title Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci
Risk Allele A
P-val 1E-40
Odds Ratio NR NR
GWAS snp
PMID [PMID 18794853OA-icon.png]
Trait Rheumatoid arthritis
Title Common variants at CD40 and other loci confer risk of rheumatoid arthritis
Risk Allele
P-val 6.0000000000000005E-42
Odds Ratio 1.79 [1.65-1.94]
GWAS snp
PMID [PMID 17554260OA-icon.png]
Trait Type 1 diabetes
Title Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
Risk Allele A
P-val 7.9999999999999994E-24
Odds Ratio 1.89 [1.67-2.13]


[PMID 19565500OA-icon.png] Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis




[PMID 22493691OA-icon.png] Novel associations for hypothyroidism include known autoimmune risk Loci.

[PMID 18224312OA-icon.png] Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment.

[PMID 18274536OA-icon.png] Genome-wide association studies: progress and potential for drug discovery and development.

[PMID 18533027OA-icon.png] Worldwide population differentiation at disease-associated SNPs.

[PMID 18853133OA-icon.png] Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.

[PMID 19168599OA-icon.png] Type 1 diabetes in the BB rat: a polygenic disease.

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

[PMID 19639606OA-icon.png] Correcting "winner's curse" in odds ratios from genomewide association findings for major complex human diseases.

[PMID 19956648OA-icon.png] Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases.

[PMID 20017963OA-icon.png] Representation of genetic association via attributable familial relative risks in order to identify polymorphisms functionally relevant to rheumatoid arthritis.

[PMID 20089178OA-icon.png] Allelic variants in the PHTF1-PTPN22, C12orf30 and CD226 regions as candidate susceptibility factors for the type 1 diabetes in the Estonian population.

[PMID 20722033OA-icon.png] The susceptibility loci juvenile idiopathic arthritis shares with other autoimmune diseases extend to PTPN2, COG6, and ANGPT1.

[PMID 20808825OA-icon.png] Novel association strategy with copy number variation for identifying new risk Loci of human diseases.


GET Evidence
rs6679677
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.0703125
summary



GWAS snp
PMID [PMID 23128233OA-icon.png]
Trait Crohn's disease
Title Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Risk Allele C
P-val 2E-15
Odds Ratio 1.20 [1.129-1.268]