rs12452509

Homo sapiens
G>A
MED1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0368 (10919/29604,GnomAD)
G==0448 (13064/29118,TOPMED)
G==0361 (1807/5008,1000G)
G==0254 (980/3854,ALSPAC)
G==0264 (978/3708,TWINSUK)
chr17:39418469 (GRCh38.p7) (17q12)
AD
GWASdb2
1   publication(s)
See rs on genome
37 Enhancers around
62 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.39418469G>A
GRCh37.p13 chr 17NC_000017.10:g.37574722G>A
MED1 RefSeqGeneNG_046996.1:g.37812C>T

Gene: MED1, mediator complex subunit 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
MED1 transcriptNM_004774.3:c.N/AIntron Variant
MED1 transcript variant X1XM_005257465.3:c.N/AIntron Variant
MED1 transcript variant X3XM_006721957.1:c.N/AIntron Variant
MED1 transcript variant X2XM_017024779.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.717A=0.283
1000GenomesAmericanSub694G=0.340A=0.660
1000GenomesEast AsianSub1008G=0.262A=0.738
1000GenomesEuropeSub1006G=0.251A=0.749
1000GenomesGlobalStudy-wide5008G=0.361A=0.639
1000GenomesSouth AsianSub978G=0.110A=0.890
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.254A=0.746
The Genome Aggregation DatabaseAfricanSub8644G=0.665A=0.335
The Genome Aggregation DatabaseAmericanSub838G=0.310A=0.690
The Genome Aggregation DatabaseEast AsianSub1604G=0.304A=0.696
The Genome Aggregation DatabaseEuropeSub18216G=0.237A=0.762
The Genome Aggregation DatabaseGlobalStudy-wide29604G=0.368A=0.631
The Genome Aggregation DatabaseOtherSub302G=0.350A=0.650
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.448A=0.551
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.264A=0.736
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs124525090.000592alcohol dependence20201924

eQTL of rs12452509 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 rs12452509 in Fetal Brain

Probe ID Position Gene beta p-value
cg07936489chr17:37558343FBXL200.01933712867080671.7063e-14
cg15445000chr17:37608096MED1-0.04612940573617265.1568e-12
cg00129232chr17:37814104STARD30.006097714374915933.4725e-10
cg20243544chr17:37824526PNMT-0.01445859032405279.5907e-10
cg07936489chr17:37558343FBXL200.0193371291.7100e-14

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 )
chr173754134337541393E067-33329
chr173755575637555808E067-18914
chr173755588837555928E067-18794
chr173755614737556212E067-18510
chr173762188337621933E06747161
chr173762213237622327E06747410
chr173753639237536664E068-38058
chr173755614737556212E068-18510
chr173762393437623984E06849212
chr173753639237536664E069-38058
chr173755614737556212E069-18510
chr173762188337621933E06947161
chr173762213237622327E06947410
chr173755575637555808E070-18914
chr173755588837555928E070-18794
chr173760526737605460E07030545
chr173760550737605677E07030785
chr173760612037606170E07031398
chr173762213237622327E07047410
chr173753639237536664E071-38058
chr173755614737556212E071-18510
chr173762213237622327E07147410
chr173755614737556212E072-18510
chr173753727237537359E074-37363
chr173753811437538164E074-36558
chr173755485837554943E081-19779
chr173755575637555808E081-18914
chr173755588837555928E081-18794
chr173755614737556212E081-18510
chr173762188337621933E08147161
chr173762213237622327E08147410
chr173762393437623984E08149212
chr173755575637555808E082-18914
chr173755588837555928E082-18794
chr173760526737605460E08230545
chr173760550737605677E08230785
chr173762213237622327E08247410









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr173755660737559334E067-15388
chr173760679237607810E06732070
chr173760811137608237E06733389
chr173761731337619882E06742591
chr173761996037620016E06745238
chr173762012337620173E06745401
chr173755660737559334E068-15388
chr173760679237607810E06832070
chr173760811137608237E06833389
chr173761705837617146E06842336
chr173761731337619882E06842591
chr173761996037620016E06845238
chr173762012337620173E06845401
chr173755660737559334E069-15388
chr173760679237607810E06932070
chr173760811137608237E06933389
chr173761731337619882E06942591
chr173761996037620016E06945238
chr173762012337620173E06945401
chr173755660737559334E070-15388
chr173760679237607810E07032070
chr173760811137608237E07033389
chr173761731337619882E07042591
chr173761996037620016E07045238
chr173762012337620173E07045401
chr173755660737559334E071-15388
chr173760679237607810E07132070
chr173760811137608237E07133389
chr173761705837617146E07142336
chr173761731337619882E07142591
chr173761996037620016E07145238
chr173762012337620173E07145401
chr173755660737559334E072-15388
chr173760679237607810E07232070
chr173760811137608237E07233389
chr173761705837617146E07242336
chr173761731337619882E07242591
chr173761996037620016E07245238
chr173762012337620173E07245401
chr173755660737559334E073-15388
chr173760679237607810E07332070
chr173760811137608237E07333389
chr173761731337619882E07342591
chr173761996037620016E07345238
chr173762012337620173E07345401
chr173755660737559334E074-15388
chr173760679237607810E07432070
chr173761705837617146E07442336
chr173761731337619882E07442591
chr173761996037620016E07445238
chr173762012337620173E07445401
chr173755660737559334E081-15388
chr173760679237607810E08132070
chr173761731337619882E08142591
chr173761996037620016E08145238
chr173762012337620173E08145401
chr173755660737559334E082-15388
chr173760679237607810E08232070
chr173760811137608237E08233389
chr173761731337619882E08242591
chr173761996037620016E08245238
chr173762012337620173E08245401