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rs4402960

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(G;G) 0 normal
(G;T) 2 1.2x increased risk for type-2 diabetes, ~1x risk for gestational diabetes
(T;T) 2.1 1.2x increased risk for type-2 diabetes, 1.5x risk for gestational diabetes
ReferenceGRCh38 38.1/141
Chromosome3
Position185793899
GeneIGF2BP2
is asnp
is mentioned by
dbSNPrs4402960
ebirs4402960
HLIrs4402960
Exacrs4402960
Varsomers4402960
Maprs4402960
PheGenIrs4402960
hapmaprs4402960
1000 genomesrs4402960
hgdprs4402960
ensemblrs4402960
gopubmedrs4402960
geneviewrs4402960
scholarrs4402960
googlers4402960
pharmgkbrs4402960
gwascentralrs4402960
openSNPrs4402960
23andMers4402960
23andMe allrs4402960
SNP Nexus

SNPshotrs4402960
SNPdbers4402960
MSV3drs4402960
GWAS Ctlgrs4402960
GMAF0.343
Max Magnitude2.1
? (G;G) (G;T) (T;T) 28

[PMID 18477659] rs4402960 replicated as significant for type-2 diabetes risk in 1,900 Japanese patients, with odds ratio of 1.23 (CI: 1.11-1.36, p = 8.1 x 10e-5)

[PMID 17463248OA-icon.png] associated with type-2 diabetes

[PMID 18162508] significantly associated with type-2 diabetes p = 0.00009; in 1,630 Japanese subjects and in 1,064 controls

[PMID 18437351] 1,638 type-2 diabetes patients and 1,858 controls

  • rs4402960 borderline (OR 1.10, 95% CI: 0.99-1.22).

[PMID 18430866OA-icon.png] Neither rs4402960 or rs1470579 were found to be associated with type-2 diabetes in a study of 3,000 French Caucasians.

[PMID 19033397OA-icon.png] This SNP was confirmed to be associated with type-2 diabetes in a study of 500+ Japanese patients plus pooled meta-analysis with 6 previous association studies (also of Japanese).

Note: rs4402960 is fairly tightly linked (r2=0.87) with another IGF2BP2 gene SNP also associated with type-2 diabetes, rs1470579

Called into question by table 1 of 10.1371/journal.pbio.1000294

GWAS
SNP rs4402960
PubMedID [PMID 17463249OA-icon.png]
Condition Type 2 diabetes
Gene IGF2BP2
Risk Allele T
pValue 9.00E-016
OR 1.14
95% CI 1.11-1.18


[PMID 19258437OA-icon.png] A Genetic Variant in the IGF2BP2 Gene may Interact with Fetal Malnutrition on Glucose Metabolism.

GWAS snp
PMID [PMID 18372903OA-icon.png]
Trait Type 2 diabetes
Title Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes
Risk Allele T
P-val 8.0000000000000002E-8
Odds Ratio 1.17 [1.10-1.25]
GWAS snp
PMID [PMID 17463246]
Trait Type 2 diabetes
Title Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels
Risk Allele T
P-val 9.0000000000000003E-16
Odds Ratio 1.14 [1.11-1.18]
GWAS snp
PMID [PMID 19401414OA-icon.png]
Trait Type 2 diabetes
Title Confirmation of multiple risk loci and genetic impacts by a genome-wide association study of type 2 diabetes in the Japanese population
Risk Allele T
P-val 0.000001
Odds Ratio 1.14 [1.08-1.21]
OMIM608289
DescINSULIN-LIKE GROWTH FACTOR 2 mRNA-BINDING PROTEIN 2; IGF2BP2
Variant
Relatedalso
[PMID 20043145OA-icon.png] Improvements in glucose homeostasis in response to regular exercise are influenced by the PPARG Pro12Ala variant: results from the HERITAGE Family Study


[PMID 20215779] Evidence of Interaction between Type 2 Diabetes Susceptibility Genes and Dietary Fat Intake for Adiposity and Glucose Homeostasis-Related Phenotypes


[PMID 20523342OA-icon.png] IGF2BP2 variations influence repaglinide response and risk of type 2 diabetes in Chinese population

[PMID 20384434] Combining genetic markers and clinical risk factors improves the risk assessment of impaired glucose metabolism

[PMID 20802253OA-icon.png] Glycemia determines the effect of type 2 diabetes risk genes on insulin secretion







OMIM608289
Desc
Variant0001
Relatedalso


[PMID 22032244] IGF2BP2 Genetic Variation and Type 2 Diabetes: A Global Meta-Analysis


[PMID 22096510OA-icon.png] Association of six single nucleotide polymorphisms with gestational diabetes mellitus in a chinese population


[PMID 22419714] Effect of Type 2 Diabetes Predisposing Genetic Variants on Colorectal Cancer Risk


[PMID 22569928OA-icon.png] Analysis of common type 2 diabetes mellitus genetic risk factors in new-onset diabetes after transplantation in kidney transplant patients medicated with tacrolimus


[PMID 17786212OA-icon.png] Heterogeneity in meta-analyses of genome-wide association investigations.


[PMID 17827400] Studies of association of variants near the HHEX, CDKN2A/B, and IGF2BP2 genes with type 2 diabetes and impaired insulin release in 10,705 Danish subjects: validation and extension of genome-wide association studies.


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


[PMID 18264689] Polymorphisms in the TCF7L2, CDKAL1 and SLC30A8 genes are associated with impaired proinsulin conversion.


[PMID 18319073OA-icon.png] Using the optimal receiver operating characteristic curve to design a predictive genetic test, exemplified with type 2 diabetes.


[PMID 18423522OA-icon.png] Estimating odds ratios in genome scans: an approximate conditional likelihood approach.


[PMID 18426861OA-icon.png] Association analysis of type 2 diabetes Loci in type 1 diabetes.


[PMID 18443202OA-icon.png] Association analysis in african americans of European-derived type 2 diabetes single nucleotide polymorphisms from whole-genome association studies.


[PMID 18461161OA-icon.png] Post genome-wide association studies of novel genes associated with type 2 diabetes show gene-gene interaction and high predictive value.


[PMID 18469204OA-icon.png] Implication of genetic variants near TCF7L2, SLC30A8, HHEX, CDKAL1, CDKN2A/B, IGF2BP2, and FTO in type 2 diabetes and obesity in 6,719 Asians.


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


[PMID 18544707OA-icon.png] Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.


[PMID 18591388OA-icon.png] Assessing the combined impact of 18 common genetic variants of modest effect sizes on type 2 diabetes risk.


[PMID 18633108OA-icon.png] Common variants in CDKAL1, CDKN2A/B, IGF2BP2, SLC30A8, and HHEX/IDE genes are associated with type 2 diabetes and impaired fasting glucose in a Chinese Han population.


[PMID 18689899OA-icon.png] Exchangeable models of complex inherited diseases.


[PMID 18694974OA-icon.png] Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study.


[PMID 18782870OA-icon.png] Clinical review: the genetics of type 2 diabetes: a realistic appraisal in 2008.


[PMID 18852197OA-icon.png] Metabolic and cardiovascular traits: an abundance of recently identified common genetic variants.


[PMID 18991055] Association between polymorphisms in SLC30A8, HHEX, CDKN2A/B, IGF2BP2, FTO, WFS1, CDKAL1, KCNQ1 and type 2 diabetes in the Korean population.


[PMID 19002430] Type 2 diabetes-associated genetic variants discovered in the recent genome-wide association studies are related to gestational diabetes mellitus in the Korean population.


[PMID 19008344OA-icon.png] Association analysis of variation in/near FTO, CDKAL1, SLC30A8, HHEX, EXT2, IGF2BP2, LOC387761, and CDKN2B with type 2 diabetes and related quantitative traits in Pima Indians.


[PMID 19056611OA-icon.png] Adiposity-related heterogeneity in patterns of type 2 diabetes susceptibility observed in genome-wide association data.


[PMID 19096518OA-icon.png] Novel association of HK1 with glycated hemoglobin in a non-diabetic population: a genome-wide evaluation of 14,618 participants in the Women's Genome Health Study.


[PMID 19207020OA-icon.png] Meta-analysis in genome-wide association studies.


[PMID 19228808OA-icon.png] Type 2 diabetes risk alleles are associated with reduced size at birth.


[PMID 19279076OA-icon.png] Genetic predisposition, Western dietary pattern, and the risk of type 2 diabetes in men.


[PMID 19323962OA-icon.png] Genome-wide association studies in type 2 diabetes.


[PMID 19324937OA-icon.png] Previously associated type 2 diabetes variants may interact with physical activity to modify the risk of impaired glucose regulation and type 2 diabetes: a study of 16,003 Swedish adults.


[PMID 19341491OA-icon.png] Genome-based prediction of common diseases: methodological considerations for future research.


[PMID 19455305OA-icon.png] No association of multiple type 2 diabetes loci with type 1 diabetes.


[PMID 19460916OA-icon.png] Genetic architecture of type 2 diabetes: recent progress and clinical implications.


[PMID 19502414OA-icon.png] Association of 18 confirmed susceptibility loci for type 2 diabetes with indices of insulin release, proinsulin conversion, and insulin sensitivity in 5,327 nondiabetic Finnish men.


[PMID 19526209OA-icon.png] Is the thrifty genotype hypothesis supported by evidence based on confirmed type 2 diabetes- and obesity-susceptibility variants?


[PMID 19602701OA-icon.png] Underlying genetic models of inheritance in established type 2 diabetes associations.


[PMID 19741467] Association of common type 2 diabetes risk gene variants and posttransplantation diabetes mellitus in renal allograft recipients in Korea.


[PMID 19902174OA-icon.png] Diet-induced gene expression of isolated pancreatic islets from a polygenic mouse model of the metabolic syndrome.


[PMID 19931040OA-icon.png] Simultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.


[PMID 19956539OA-icon.png] How many genetic variants remain to be discovered?


[PMID 20017978OA-icon.png] Influence of control selection in genome-wide association studies: the example of diabetes in the Framingham Heart Study.


[PMID 20018066OA-icon.png] Epistatic interactions of CDKN2B-TCF7L2 for risk of type 2 diabetes and of CDKN2B-JAZF1 for triglyceride/high-density lipoprotein ratio longitudinal change: evidence from the Framingham Heart Study.


[PMID 20049090OA-icon.png] Association between type 2 diabetes loci and measures of fatness.


[PMID 20126254OA-icon.png] Rare variants create synthetic genome-wide associations.


[PMID 20142250OA-icon.png] Diabetes genes and prostate cancer in the Atherosclerosis Risk in Communities study.


[PMID 20144327OA-icon.png] A genomics study of type 2 diabetes mellitus in U.S. Air Force personnel.


[PMID 20161779OA-icon.png] Investigation of type 2 diabetes risk alleles support CDKN2A/B, CDKAL1, and TCF7L2 as susceptibility genes in a Han Chinese cohort.


[PMID 20424228OA-icon.png] Impact of common variants of PPARG, KCNJ11, TCF7L2, SLC30A8, HHEX, CDKN2A, IGF2BP2, and CDKAL1 on the risk of type 2 diabetes in 5,164 Indians.


[PMID 20509872OA-icon.png] Implication of genetic variants near SLC30A8, HHEX, CDKAL1, CDKN2A/B, IGF2BP2, FTO, TCF2, KCNQ1, and WFS1 in type 2 diabetes in a Chinese population.


[PMID 20532014OA-icon.png] The epidemiology of diabetes in Korea: from the economics to genetics.


[PMID 20550665OA-icon.png] Association study of genetic variants in eight genes/loci with type 2 diabetes in a Han Chinese population.


[PMID 20712903OA-icon.png] Obesity and diabetes genes are associated with being born small for gestational age: results from the Auckland Birthweight Collaborative study.


[PMID 21278902OA-icon.png] Genetic risk profiling for prediction of type 2 diabetes.


[PMID 21283728OA-icon.png] Genetic variants of diabetes risk and incident cardiovascular events in chronic coronary artery disease.


[PMID 22015911] Quantitative assessment of the variation in IGF2BP2 gene and type 2 diabetes risk.


[PMID 22245690] Strong association of common variants in the IGF2BP2 gene with type 2 diabetes in Lebanese Arabs.

GWAS snp
PMID [PMID 22693455OA-icon.png]
Trait
Title Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.
Risk Allele T
P-val 3E-9
Odds Ratio 1.1500 None


GET Evidence
rs4402960
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.335938
summary



[PMID 23403707OA-icon.png] The rs11705701 G>A Polymorphism of IGF2BP2 is Associated With IGF2BP2 mRNA and Protein Levels in the Visceral Adipose Tissue - A Link to Type 2 Diabetes Susceptibility


[PMID 23029294OA-icon.png] Meta-analysis of the relationship between common type 2 diabetes risk gene variants with gestational diabetes mellitus


[PMID 23690305OA-icon.png] Genetic variants and the risk of gestational diabetes mellitus: a systematic review


[PMID 22923468OA-icon.png] Contribution of common genetic variation to the risk of type 2 diabetes in the Mexican Mestizo population.


[PMID 23298195] Association study of genetic variants of 17 diabetes-related genes/loci and cardiovascular risk and diabetic nephropathy in the Chinese She population.


[PMID 23458876] ACE I/D and MTHFR C677T polymorphisms are significantly associated with type 2 diabetes in Arab ethnicity: a meta-analysis.


[PMID 25062844OA-icon.png] IGF2BP2 and obesity interaction analysis for type 2 diabetes mellitus in chinese han population

GWAS snp
PMID [PMID 24509480OA-icon.png]
Trait Type 2 diabetes
Title Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
Risk Allele T
P-val 1E-17
Odds Ratio 1.13 [1.09-1.17]


ClinVar
Risk rs4402960(T;T)
Alt rs4402960(T;T)
Reference rs4402960(G;G)
Significance Other
Disease Diabetes mellitus type 2
Variation info
Gene IGF2BP2
CLNDBN Diabetes mellitus type 2
Reversed 0
HGVS NC_000003.11:g.185511687G>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000002537.2,



[PMID 24959828OA-icon.png] Genetic association study with metabolic syndrome and metabolic-related traits in a cross-sectional sample and a 10-year longitudinal sample of chinese elderly population


[PMID 25755232] Habitual coffee intake, genetic polymorphisms, and type 2 diabetes


[PMID 27310578] Replication and Relevance of Multiple Susceptibility Loci Discovered from Genome Wide Association Studies for Type 2 Diabetes in an Indian Population.