rs2229882

Homo sapiens
C>T
MAP3K1 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0047 (5720/120570,ExAC)
T=0041 (1233/29980,GnomAD)
T=0043 (1273/29118,TOPMED)
C==0047 (567/11974,GO-ESP)
T=0045 (223/5008,1000G)
T=0057 (219/3854,ALSPAC)
T=0046 (172/3708,TWINSUK)
chr5:56872885 (GRCh38.p7) (5q11.2)
AD
GWASdb2
3   publication(s)
See rs on genome
99 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.56872885C>T
GRCh37.p13 chr 5NC_000005.9:g.56168712C>T
MAP3K1 RefSeqGeneNG_031884.1:g.62813C>T

Gene: MAP3K1, mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MAP3K1 transcriptNM_005921.1:c.156...NM_005921.1:c.1566C>TT [ACC]> T [ACT]Coding Sequence Variant
mitogen-activated protein kinase kinase kinase 1NP_005912.1:p.Thr...NP_005912.1:p.Thr522=T [Thr]> T [Thr]Synonymous Variant
MAP3K1 transcript variant X2XM_017009484.1:c....XM_017009484.1:c.1155C>TT [ACC]> T [ACT]Coding Sequence Variant
mitogen-activated protein kinase kinase kinase 1 isoform X1XP_016864973.1:p....XP_016864973.1:p.Thr385=T [Thr]> T [Thr]Synonymous Variant
MAP3K1 transcript variant X3XM_017009485.1:c....XM_017009485.1:c.1077C>TT [ACC]> T [ACT]Coding Sequence Variant
mitogen-activated protein kinase kinase kinase 1 isoform X2XP_016864974.1:p....XP_016864974.1:p.Thr359=T [Thr]> T [Thr]Synonymous Variant
MAP3K1 transcript variant X1XR_001742068.1:n....XR_001742068.1:n.1596C>TC>TNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.969T=0.031
1000GenomesAmericanSub694C=0.940T=0.060
1000GenomesEast AsianSub1008C=0.938T=0.062
1000GenomesEuropeSub1006C=0.951T=0.049
1000GenomesGlobalStudy-wide5008C=0.955T=0.045
1000GenomesSouth AsianSub978C=0.970T=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.943T=0.057
The Exome Aggregation ConsortiumAmericanSub21328C=0.949T=0.050
The Exome Aggregation ConsortiumAsianSub25098C=0.963T=0.036
The Exome Aggregation ConsortiumEuropeSub73246C=0.949T=0.050
The Exome Aggregation ConsortiumGlobalStudy-wide120570C=0.952T=0.047
The Exome Aggregation ConsortiumOtherSub898C=0.960T=0.040
The Genome Aggregation DatabaseAfricanSub8732C=0.967T=0.033
The Genome Aggregation DatabaseAmericanSub836C=0.950T=0.050
The Genome Aggregation DatabaseEast AsianSub1616C=0.945T=0.055
The Genome Aggregation DatabaseEuropeSub18494C=0.956T=0.043
The Genome Aggregation DatabaseGlobalStudy-wide29980C=0.958T=0.041
The Genome Aggregation DatabaseOtherSub302C=0.940T=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.956T=0.043
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.954T=0.046
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
27572337Association study confirms two susceptibility loci for breast cancer in Chinese Han women.Xu MBreast Cancer Res Treat
24493630A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age.Ahsan HCancer Epidemiol Biomarkers Prev

P-Value

SNP ID p-value Traits Study
rs22298820.00038alcohol dependence(early age of onset)20201924
rs22298820.00054alcohol dependence20201924

eQTL of rs2229882 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs2229882 in Fetal Brain

Probe ID Position Gene beta p-value
cg25148456chr5:56109540MAP3K10.1240182883183855.5361e-13

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 )
chr55611899256119318E067-49394
chr55613487556135001E067-33711
chr55621606956216408E06747357
chr55611899256119318E068-49394
chr55612206756122131E068-46581
chr55612234056122690E068-46022
chr55612269956122779E068-45933
chr55612282156123353E068-45359
chr55612373056123809E068-44903
chr55612389456123963E068-44749
chr55612484456125473E068-43239
chr55612548456125638E068-43074
chr55612576056125837E068-42875
chr55612629056126349E068-42363
chr55613197256132012E068-36700
chr55613202656132080E068-36632
chr55613231756132456E068-36256
chr55613260256132715E068-35997
chr55613298656133037E068-35675
chr55613323356133504E068-35208
chr55613356056133650E068-35062
chr55613391456134846E068-33866
chr55613487556135001E068-33711
chr55614078556140878E068-27834
chr55614106256141151E068-27561
chr55614123456141371E068-27341
chr55614416656144339E068-24373
chr55614722956147939E068-20773
chr55614796356148221E068-20491
chr55614956456149826E068-18886
chr55614984356149893E068-18819
chr55615050756150728E068-17984
chr55611899256119318E069-49394
chr55613391456134846E069-33866
chr55614416656144339E069-24373
chr55621606956216408E06947357
chr55612484456125473E070-43239
chr55612548456125638E070-43074
chr55612576056125837E070-42875
chr55613323356133504E070-35208
chr55613356056133650E070-35062
chr55613391456134846E070-33866
chr55613487556135001E070-33711
chr55615251056152654E070-16058
chr55612269956122779E071-45933
chr55612282156123353E071-45359
chr55612373056123809E071-44903
chr55612389456123963E071-44749
chr55612484456125473E071-43239
chr55612548456125638E071-43074
chr55612576056125837E071-42875
chr55612811956128218E071-40494
chr55612832156128409E071-40303
chr55613260256132715E071-35997
chr55613298656133037E071-35675
chr55613323356133504E071-35208
chr55613356056133650E071-35062
chr55613391456134846E071-33866
chr55613487556135001E071-33711
chr55614722956147939E071-20773
chr55611899256119318E072-49394
chr55612125356121591E072-47121
chr55612548456125638E072-43074
chr55613391456134846E072-33866
chr55615050756150728E072-17984
chr55621606956216408E07247357
chr55612234056122690E073-46022
chr55612269956122779E073-45933
chr55612282156123353E073-45359
chr55612373056123809E073-44903
chr55612389456123963E073-44749
chr55613260256132715E073-35997
chr55613298656133037E073-35675
chr55613323356133504E073-35208
chr55613356056133650E073-35062
chr55613391456134846E073-33866
chr55613487556135001E073-33711
chr55614722956147939E073-20773
chr55614796356148221E073-20491
chr55612206756122131E074-46581
chr55612234056122690E074-46022
chr55612269956122779E074-45933
chr55612282156123353E074-45359
chr55612484456125473E074-43239
chr55612548456125638E074-43074
chr55612576056125837E074-42875
chr55612924056129429E074-39283
chr55612946256129502E074-39210
chr55613298656133037E074-35675
chr55613323356133504E074-35208
chr55613356056133650E074-35062
chr55613391456134846E074-33866
chr55613487556135001E074-33711
chr55614123456141371E074-27341
chr55614416656144339E074-24373
chr55614722956147939E074-20773
chr55614796356148221E074-20491
chr55615251056152654E074-16058
chr55621606956216408E07447357








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr55620433056206896E06735618
chr55620433056206896E06835618
chr55620433056206896E06935618
chr55620433056206896E07035618
chr55620433056206896E07135618
chr55620433056206896E07235618
chr55620433056206896E07335618
chr55620433056206896E07435618
chr55620433056206896E08135618
chr55620433056206896E08235618