rs7297499

Homo sapiens
T>C
CCNT1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0037 (1115/29936,GnomAD)
C=0049 (1437/29118,TOPMED)
C=0029 (146/5008,1000G)
C=0022 (86/3854,ALSPAC)
C=0025 (91/3708,TWINSUK)
chr12:48706067 (GRCh38.p7) (12q13.12)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.48706067T>C
GRCh37.p13 chr 12NC_000012.11:g.49099850T>C

Gene: CCNT1, cyclin T1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CCNT1 transcript variant aNM_001240.3:c.N/AIntron Variant
CCNT1 transcript variant bNM_001277842.1:c.N/AIntron Variant
CCNT1 transcript variant X1XM_017020197.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.928C=0.072
1000GenomesAmericanSub694T=0.990C=0.010
1000GenomesEast AsianSub1008T=1.000C=0.000
1000GenomesEuropeSub1006T=0.964C=0.036
1000GenomesGlobalStudy-wide5008T=0.971C=0.029
1000GenomesSouth AsianSub978T=0.990C=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.978C=0.022
The Genome Aggregation DatabaseAfricanSub8704T=0.928C=0.072
The Genome Aggregation DatabaseAmericanSub836T=0.980C=0.020
The Genome Aggregation DatabaseEast AsianSub1614T=0.999C=0.001
The Genome Aggregation DatabaseEuropeSub18482T=0.974C=0.025
The Genome Aggregation DatabaseGlobalStudy-wide29936T=0.962C=0.037
The Genome Aggregation DatabaseOtherSub300T=0.970C=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.950C=0.049
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.975C=0.025
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
rs72974990.0000597alcoholismpha002891
rs72974990.0000597alcohol dependence20201924

eQTL of rs7297499 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 rs7297499 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

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 )
chr124907263249072783E067-27067
chr124907279549072924E067-26926
chr124907322449073379E067-26471
chr124907343949073502E067-26348
chr124907353449073617E067-26233
chr124907372449073844E067-26006
chr124907388049073934E067-25916
chr124907401049074163E067-25687
chr124907428149074321E067-25529
chr124910761449107693E0677764
chr124910774049107825E0677890
chr124910819549108258E0678345
chr124910843049108484E0678580
chr124910860049108679E0678750
chr124907111449071290E068-28560
chr124907160349071855E068-27995
chr124907189349071976E068-27874
chr124907197949072101E068-27749
chr124907227349072326E068-27524
chr124907233149072381E068-27469
chr124907246249072600E068-27250
chr124907343949073502E068-26348
chr124907353449073617E068-26233
chr124907372449073844E068-26006
chr124907388049073934E068-25916
chr124910819549108258E0688345
chr124910843049108484E0688580
chr124910860049108679E0688750
chr124907160349071855E069-27995
chr124907189349071976E069-27874
chr124907197949072101E069-27749
chr124907227349072326E069-27524
chr124907233149072381E069-27469
chr124907246249072600E069-27250
chr124907263249072783E069-27067
chr124907279549072924E069-26926
chr124907322449073379E069-26471
chr124907343949073502E069-26348
chr124907353449073617E069-26233
chr124907372449073844E069-26006
chr124907388049073934E069-25916
chr124907401049074163E069-25687
chr124907428149074321E069-25529
chr124910740349107463E0697553
chr124910752649107576E0697676
chr124910761449107693E0697764
chr124910774049107825E0697890
chr124907105049071101E070-28749
chr124907111449071290E070-28560
chr124907160349071855E070-27995
chr124907189349071976E070-27874
chr124907197949072101E070-27749
chr124907227349072326E070-27524
chr124907233149072381E070-27469
chr124907246249072600E070-27250
chr124907263249072783E070-27067
chr124907279549072924E070-26926
chr124910740349107463E0707553
chr124910752649107576E0707676
chr124910761449107693E0707764
chr124910774049107825E0707890
chr124910819549108258E0708345
chr124910843049108484E0708580
chr124907197949072101E071-27749
chr124907227349072326E071-27524
chr124907233149072381E071-27469
chr124907246249072600E071-27250
chr124907263249072783E071-27067
chr124907279549072924E071-26926
chr124907322449073379E071-26471
chr124907343949073502E071-26348
chr124907353449073617E071-26233
chr124907372449073844E071-26006
chr124907388049073934E071-25916
chr124907401049074163E071-25687
chr124907189349071976E072-27874
chr124907197949072101E072-27749
chr124907246249072600E072-27250
chr124907263249072783E072-27067
chr124907279549072924E072-26926
chr124907322449073379E072-26471
chr124907343949073502E072-26348
chr124907353449073617E072-26233
chr124907372449073844E072-26006
chr124907263249072783E073-27067
chr124907279549072924E073-26926
chr124907322449073379E073-26471
chr124907343949073502E073-26348
chr124907353449073617E073-26233
chr124907372449073844E073-26006
chr124907388049073934E073-25916
chr124907401049074163E073-25687
chr124907428149074321E073-25529
chr124907160349071855E074-27995
chr124907189349071976E074-27874
chr124907197949072101E074-27749
chr124907227349072326E074-27524
chr124907233149072381E074-27469
chr124907246249072600E074-27250
chr124907263249072783E074-27067
chr124907279549072924E074-26926
chr124907322449073379E074-26471
chr124907343949073502E074-26348
chr124907353449073617E074-26233
chr124907372449073844E074-26006
chr124907388049073934E074-25916
chr124907401049074163E074-25687
chr124907105049071101E081-28749
chr124907111449071290E081-28560
chr124907263249072783E081-27067
chr124907279549072924E081-26926
chr124907322449073379E081-26471
chr124907343949073502E081-26348
chr124907353449073617E081-26233
chr124907372449073844E081-26006
chr124907388049073934E081-25916
chr124907401049074163E081-25687
chr124907428149074321E081-25529
chr124910843049108484E0818580
chr124910860049108679E0818750
chr124907227349072326E082-27524
chr124907233149072381E082-27469
chr124907246249072600E082-27250
chr124910819549108258E0828345










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr124907500149075085E067-24765
chr124907513749076490E067-23360
chr124910950649109686E0679656
chr124910969849110986E0679848
chr124911104149111700E06711191
chr124907484749074897E068-24953
chr124907500149075085E068-24765
chr124907513749076490E068-23360
chr124907666349076728E068-23122
chr124910950649109686E0689656
chr124910969849110986E0689848
chr124911104149111700E06811191
chr124907500149075085E069-24765
chr124907513749076490E069-23360
chr124910950649109686E0699656
chr124910969849110986E0699848
chr124911104149111700E06911191
chr124907484749074897E070-24953
chr124907500149075085E070-24765
chr124907513749076490E070-23360
chr124907666349076728E070-23122
chr124910950649109686E0709656
chr124910969849110986E0709848
chr124911104149111700E07011191
chr124907500149075085E071-24765
chr124907513749076490E071-23360
chr124907666349076728E071-23122
chr124910969849110986E0719848
chr124911104149111700E07111191
chr124907484749074897E072-24953
chr124907500149075085E072-24765
chr124907513749076490E072-23360
chr124907666349076728E072-23122
chr124907689649077002E072-22848
chr124910950649109686E0729656
chr124910969849110986E0729848
chr124911104149111700E07211191
chr124907500149075085E073-24765
chr124907513749076490E073-23360
chr124910950649109686E0739656
chr124910969849110986E0739848
chr124911104149111700E07311191
chr124907500149075085E074-24765
chr124907513749076490E074-23360
chr124910969849110986E0749848
chr124911104149111700E07411191
chr124907484749074897E081-24953
chr124907500149075085E081-24765
chr124907513749076490E081-23360
chr124911104149111700E08111191
chr124907484749074897E082-24953
chr124907500149075085E082-24765
chr124907513749076490E082-23360
chr124907666349076728E082-23122
chr124910950649109686E0829656
chr124910969849110986E0829848
chr124911104149111700E08211191