rs2424913

Homo sapiens
C>T
DNMT3B : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0442 (53046/119906,ExAC)
C==0468 (14028/29938,GnomAD)
C==0447 (13033/29118,TOPMED)
T=0492 (6395/12998,GO-ESP)
C==0312 (1562/5008,1000G)
T=0456 (1758/3854,ALSPAC)
T=0439 (1627/3708,TWINSUK)
chr20:32786453 (GRCh38.p7) (20q11.21)
ND
GWASdb2
28   publication(s)
See rs on genome
154 Enhancers around
28 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.32786453C>T
GRCh37.p13 chr 20NC_000020.10:g.31374259C>T
DNMT3B RefSeqGene LRG_56

Gene: DNMT3B, DNA (cytosine-5-)-methyltransferase 3 beta(plus strand)

Molecule type Change Amino acid[Codon] SO Term
DNMT3B transcript variant 7NM_001207055.1:c.N/AIntron Variant
DNMT3B transcript variant 8NM_001207056.1:c.N/AIntron Variant
DNMT3B transcript variant 1NM_006892.3:c.N/AIntron Variant
DNMT3B transcript variant 2NM_175848.1:c.N/AIntron Variant
DNMT3B transcript variant 3NM_175849.1:c.N/AIntron Variant
DNMT3B transcript variant 6NM_175850.2:c.N/AIntron Variant
DNMT3B transcript variant X1XM_011528653.2:c.N/AIntron Variant
DNMT3B transcript variant X2XM_011528654.2:c.N/AIntron Variant
DNMT3B transcript variant X3XR_936510.2:n.N/AIntron Variant
DNMT3B transcript variant X4XR_936511.2:n.N/AIntron Variant
DNMT3B transcript variant X5XR_936512.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.325T=0.675
1000GenomesAmericanSub694C=0.360T=0.640
1000GenomesEast AsianSub1008C=0.007T=0.993
1000GenomesEuropeSub1006C=0.587T=0.413
1000GenomesGlobalStudy-wide5008C=0.312T=0.688
1000GenomesSouth AsianSub978C=0.290T=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.544T=0.456
The Exome Aggregation ConsortiumAmericanSub21706C=0.307T=0.692
The Exome Aggregation ConsortiumAsianSub25092C=0.223T=0.776
The Exome Aggregation ConsortiumEuropeSub72212C=0.558T=0.441
The Exome Aggregation ConsortiumGlobalStudy-wide119906C=0.442T=0.557
The Exome Aggregation ConsortiumOtherSub896C=0.490T=0.510
The Genome Aggregation DatabaseAfricanSub8714C=0.372T=0.628
The Genome Aggregation DatabaseAmericanSub834C=0.310T=0.690
The Genome Aggregation DatabaseEast AsianSub1622C=0.004T=0.996
The Genome Aggregation DatabaseEuropeSub18466C=0.560T=0.439
The Genome Aggregation DatabaseGlobalStudy-wide29938C=0.468T=0.531
The Genome Aggregation DatabaseOtherSub302C=0.530T=0.470
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.447T=0.552
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.561T=0.439
PMID Title Author Journal
22009713Genetic sequence variants and the development of secondary primary cancers in patients with head and neck cancers.Azad AKCancer
25038421DNA methyltransferase haplotype is associated with Alzheimer's disease.Pezzi JCNeurosci Lett
20960050Dietary methyl donors, methyl metabolizing enzymes, and epigenetic regulators: diet-gene interactions and promoter CpG island hypermethylation in colorectal cancer.de Vogel SCancer Causes Control
28041964Association between DNA methyltransferase gene polymorphism and Parkinson's disease.Pezzi JCNeurosci Lett
27699015Association of DNA methyltransferase polymorphisms with susceptibility to primary gouty arthritis.Zhong XBiomed Rep
20593030Human intelligence and polymorphisms in the DNA methyltransferase genes involved in epigenetic marking.Haggarty PPLoS One
27590349Association of DNA Methyltransferase 3B Promotor Polymorphism With Childhood Chronic Immune Thrombocytopenia.Gouda HMLab Med
22488850Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.Zuo LAm J Med Genet B Neuropsychiatr Genet
18499700Haplotypes of DNMT1 and DNMT3B are associated with mutagen sensitivity induced by benzo[a]pyrene diol epoxide among smokers.Leng SCarcinogenesis
18455294Polymorphisms of the DNMT3B gene and risk of squamous cell carcinoma of the head and neck: a case-control study.Liu ZCancer Lett
24362509DNMT3B C46359T and SHMT1 C1420T polymorphisms in the folate pathway in carcinogenesis of head and neck.Succi MMol Biol Rep
19798569Two-stage case-control study of DNMT-1 and DNMT-3B gene variants and breast cancer risk.Ye CBreast Cancer Res Treat
21247820Polymorphisms in arsenic(+III oxidation state) methyltransferase (AS3MT) predict gene expression of AS3MT as well as arsenic metabolism.Engstrom KEnviron Health Perspect
23666104DNMT1, DNMT3A and DNMT3B gene variants in relation to ovarian cancer risk in the Polish population.Mostowska AMol Biol Rep
23081874DNMT3B promoter polymorphisms and maternal risk of birth of a child with Down syndrome.Coppede FHum Reprod
25656965Maternal risk for down syndrome and polymorphisms in the promoter region of the DNMT3B gene: a case-control study.Jaiswal SKBirth Defects Res A Clin Mol Teratol
24967710Epigenetic genes and emotional reactivity to daily life events: a multi-step gene-environment interaction study.Pishva EPLoS One
21519807Genetic variation in the promoter of DNMT3B is associated with the risk of colorectal cancer.Bao QInt J Colorectal Dis
27237591Gene-gene and gene-sex epistatic interactions of DNMT1, DNMT3A and DNMT3B in autoimmune thyroid disease.Cai TTEndocr J
22272627DNMT3B promoter polymorphisms and risk of late onset Alzheimer's disease.Coppede FCurr Alzheimer Res
19465161Single nucleotide polymorphism in DNMT3B promoter and its association with hepatocellular carcinoma in a Moroccan population.Ezzikouri SInfect Genet Evol
24859147DNA methyl transferase (DNMT) gene polymorphisms could be a primary event in epigenetic susceptibility to schizophrenia.Saradalekshmi KRPLoS One
24500500Gene promoter methylation in colorectal cancer and healthy adjacent mucosa specimens: correlation with physiological and pathological characteristics, and with biomarkers of one-carbon metabolism.Coppede FEpigenetics
25515408Systematic evaluation of cancer risk associated with DNMT3B polymorphisms.Duan FJ Cancer Res Clin Oncol
23951366Application of artificial neural networks to investigate one-carbon metabolism in Alzheimer's disease and healthy matched individuals.Coppede FPLoS One
22091311DNA-methyltransferase 3B 39179 G > T polymorphism and risk of sporadic colorectal cancer in a subset of Iranian population.Daraei AJ Res Med Sci
22382075Low-level environmental cadmium exposure is associated with DNA hypomethylation in Argentinean women.Hossain MBEnviron Health Perspect
22942708Risk-association of DNA methyltransferases polymorphisms with gastric cancer in the Southern Chinese population.Yang XXInt J Mol Sci

P-Value

SNP ID p-value Traits Study
rs24249135.4E-06alcohol and nictotine co-dependence22488850

eQTL of rs2424913 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr20:31374259DNMT3BENSG00000088305.14C>T6.2055e-1024068Cerebellum
Chr20:31374259DNMT3BENSG00000088305.14C>T8.0712e-924068Cerebellar_Hemisphere
Chr20:31374259DNMT3BENSG00000088305.14C>T1.6035e-324068Anterior_cingulate_cortex

meQTL of rs2424913 in Fetal Brain

Probe ID Position Gene beta p-value
cg13636640chr20:31349939DNMT3B-0.07147307798763055.5240e-19

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr203136829131369331E067-4928
chr203137773431378287E0673475
chr203137838831378478E0674129
chr203140922531409736E06734966
chr203140980931410121E06735550
chr203141019131410327E06735932
chr203141039031411358E06736131
chr203141577331415976E06741514
chr203141597831416162E06741719
chr203141621031416310E06741951
chr203141632231416378E06742063
chr203141638531416461E06742126
chr203141646231416635E06742203
chr203141719731417789E06742938
chr203141782931417928E06743570
chr203140922531409736E06834966
chr203140980931410121E06835550
chr203141019131410327E06835932
chr203141039031411358E06836131
chr203141577331415976E06841514
chr203141597831416162E06841719
chr203141621031416310E06841951
chr203141632231416378E06842063
chr203141638531416461E06842126
chr203141646231416635E06842203
chr203141719731417789E06842938
chr203142405931424166E06849800
chr203132543531325500E069-48759
chr203132550431326081E069-48178
chr203132955431329733E069-44526
chr203136808831368217E069-6042
chr203136829131369331E069-4928
chr203137773431378287E0693475
chr203137838831378478E0694129
chr203137993131380037E0695672
chr203138004631381101E0695787
chr203140922531409736E06934966
chr203140980931410121E06935550
chr203141019131410327E06935932
chr203141039031411358E06936131
chr203141577331415976E06941514
chr203141597831416162E06941719
chr203141621031416310E06941951
chr203141632231416378E06942063
chr203141638531416461E06942126
chr203141646231416635E06942203
chr203141719731417789E06942938
chr203141782931417928E06943570
chr203140922531409736E07034966
chr203141039031411358E07036131
chr203132955431329733E071-44526
chr203136808831368217E071-6042
chr203136829131369331E071-4928
chr203137773431378287E0713475
chr203137838831378478E0714129
chr203138004631381101E0715787
chr203140922531409736E07134966
chr203141577331415976E07141514
chr203141597831416162E07141719
chr203141621031416310E07141951
chr203141632231416378E07142063
chr203141638531416461E07142126
chr203141646231416635E07142203
chr203141719731417789E07142938
chr203141782931417928E07143570
chr203141815231418211E07143893
chr203141826831418318E07144009
chr203136808831368217E072-6042
chr203136829131369331E072-4928
chr203140980931410121E07235550
chr203141039031411358E07236131
chr203141577331415976E07241514
chr203141597831416162E07241719
chr203141719731417789E07242938
chr203141782931417928E07243570
chr203141815231418211E07243893
chr203142405931424166E07249800
chr203136829131369331E073-4928
chr203140922531409736E07334966
chr203140980931410121E07335550
chr203141019131410327E07335932
chr203141577331415976E07341514
chr203141597831416162E07341719
chr203141621031416310E07341951
chr203141632231416378E07342063
chr203141638531416461E07342126
chr203141646231416635E07342203
chr203141719731417789E07342938
chr203141782931417928E07343570
chr203136829131369331E074-4928
chr203140922531409736E07434966
chr203140980931410121E07435550
chr203141577331415976E07441514
chr203141597831416162E07441719
chr203141621031416310E07441951
chr203141632231416378E07442063
chr203141638531416461E07442126
chr203141646231416635E07442203
chr203141782931417928E07443570
chr203141815231418211E07443893
chr203132955431329733E081-44526
chr203136432831364932E081-9327
chr203136494231365035E081-9224
chr203136506331365836E081-8423
chr203136609231366682E081-7577
chr203136682231367010E081-7249
chr203136705031367131E081-7128
chr203136808831368217E081-6042
chr203136829131369331E081-4928
chr203137007731370174E081-4085
chr203137063231370708E081-3551
chr203137961731379696E0815358
chr203137975131379801E0815492
chr203137981531379865E0815556
chr203137993131380037E0815672
chr203138004631381101E0815787
chr203138314631383351E0818887
chr203138335531383435E0819096
chr203138354731383608E0819288
chr203138368631383736E0819427
chr203138374331383793E0819484
chr203139418931394544E08119930
chr203140922531409736E08134966
chr203141019131410327E08135932
chr203136682231367010E082-7249
chr203136705031367131E082-7128
chr203137007731370174E082-4085
chr203137063231370708E082-3551
chr203137773431378287E0823475
chr203137838831378478E0824129
chr203137942531379569E0825166
chr203137961731379696E0825358
chr203137975131379801E0825492
chr203137981531379865E0825556
chr203137993131380037E0825672
chr203138280831382940E0828549
chr203138314631383351E0828887
chr203138335531383435E0829096
chr203138398931385414E0829730
chr203138596131386238E08211702
chr203138640531386524E08212146
chr203138656531386652E08212306
chr203139314731393342E08218888
chr203139365531393715E08219396
chr203139373131393838E08219472
chr203139384731393926E08219588
chr203139392731393977E08219668
chr203139409031394144E08219831
chr203139418931394544E08219930
chr203139486631395010E08220607
chr203139509231395167E08220833
chr203141039031411358E08236131
chr203141156631411660E08237307
chr203141174331412176E08237484










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr203133005131332373E067-41886
chr203134899231351909E067-22350
chr203140723131408788E06732972
chr203133005131332373E068-41886
chr203134899231351909E068-22350
chr203140723131408788E06832972
chr203133005131332373E069-41886
chr203134899231351909E069-22350
chr203140723131408788E06932972
chr203133005131332373E070-41886
chr203134899231351909E070-22350
chr203140723131408788E07032972
chr203133005131332373E071-41886
chr203134899231351909E071-22350
chr203140723131408788E07132972
chr203133005131332373E072-41886
chr203134899231351909E072-22350
chr203140723131408788E07232972
chr203133005131332373E073-41886
chr203134899231351909E073-22350
chr203140723131408788E07332972
chr203133005131332373E074-41886
chr203134899231351909E074-22350
chr203140723131408788E07432972
chr203133005131332373E081-41886
chr203133005131332373E082-41886
chr203134899231351909E082-22350
chr203140723131408788E08232972