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From SNPedia

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
is asnp
is mentioned by
1000 genomesrs4402960
23andMe allrs4402960
SNP Nexus

GWAS Ctlgrs4402960
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

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]
[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


[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]
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
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.335938

[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]

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.