rs2456778

Homo sapiens
A>T
CDK1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0208 (24891/119288,ExAC)
A==0217 (6472/29782,GnomAD)
A==0229 (6694/29118,TOPMED)
T=0240 (3121/12986,GO-ESP)
A==0206 (1034/5008,1000G)
A==0247 (952/3854,ALSPAC)
A==0244 (903/3708,TWINSUK)
chr10:60792132 (GRCh38.p7) (10q21.2)
CD
GWASdb2 | GWASCatalog
2   publication(s)
See rs on genome
29 Enhancers around
23 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.60792132A>T
GRCh37.p13 chr 10NC_000010.10:g.62551890A>T
CDK1 RefSeqGeneNG_029877.1:g.18802A>T

Gene: CDK1, cyclin-dependent kinase 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDK1 transcript variant 6NM_001320918.1:c.N/AIntron Variant
CDK1 transcript variant 1NM_001786.4:c.N/AIntron Variant
CDK1 transcript variant 2NM_033379.4:c.N/AIntron Variant
CDK1 transcript variant 4NM_001170406.1:c.N/AGenic Downstream Transcript Variant
CDK1 transcript variant 5NM_001170407.1:c.N/AGenic Downstream Transcript Variant
CDK1 transcript variant X1XM_005270303.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.256T=0.744
1000GenomesAmericanSub694A=0.200T=0.800
1000GenomesEast AsianSub1008A=0.157T=0.843
1000GenomesEuropeSub1006A=0.196T=0.804
1000GenomesGlobalStudy-wide5008A=0.206T=0.794
1000GenomesSouth AsianSub978A=0.210T=0.790
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.247T=0.753
The Exome Aggregation ConsortiumAmericanSub21238A=0.226T=0.773
The Exome Aggregation ConsortiumAsianSub24920A=0.176T=0.823
The Exome Aggregation ConsortiumEuropeSub72240A=0.214T=0.785
The Exome Aggregation ConsortiumGlobalStudy-wide119288A=0.208T=0.791
The Exome Aggregation ConsortiumOtherSub890A=0.200T=0.800
The Genome Aggregation DatabaseAfricanSub8658A=0.236T=0.764
The Genome Aggregation DatabaseAmericanSub834A=0.220T=0.780
The Genome Aggregation DatabaseEast AsianSub1610A=0.148T=0.852
The Genome Aggregation DatabaseEuropeSub18378A=0.214T=0.785
The Genome Aggregation DatabaseGlobalStudy-wide29782A=0.217T=0.782
The Genome Aggregation DatabaseOtherSub302A=0.200T=0.800
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.229T=0.770
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.244T=0.756
PMID Title Author Journal
27066308Dopamine pathway gene variants may modulate cognitive performance in the DHS - Mind Study.Martelle SEBrain Behav
23958962Genome-wide association study of cocaine dependence and related traits: FAM53B identified as a risk gene.Gelernter JMol Psychiatry

P-Value

SNP ID p-value Traits Study
rs24567780.000003Cocaine induced paranoia23958962
rs24567785.00E-06Cocaine induced paranoia, AA23958962

eQTL of rs2456778 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 rs2456778 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 )
chr106256995662571077E06718066
chr106257115262571377E06719262
chr106257621462577478E06724324
chr106256110362561655E0689213
chr106256995662571077E06818066
chr106257115262571377E06819262
chr106256982362569910E06917933
chr106256995662571077E06918066
chr106257621462577478E06924324
chr106254106762541474E070-10416
chr106254149762541817E070-10073
chr106256207262562145E07010182
chr106250226162502620E071-49270
chr106256995662571077E07118066
chr106257115262571377E07119262
chr106257621462577478E07124324
chr106256995662571077E07218066
chr106257115262571377E07219262
chr106257621462577478E07224324
chr106256995662571077E07318066
chr106257115262571377E07319262
chr106257621462577478E07324324
chr106250226162502620E074-49270
chr106256982362569910E07417933
chr106256995662571077E07418066
chr106257621462577478E07424324
chr106256002962560558E0818139
chr106256059762560698E0818707
chr106257621462577478E08124324









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr106253772662539398E068-12492
chr106253772662539398E069-12492
chr106253762562537684E070-14206
chr106253772662539398E070-12492
chr106253941562539475E070-12415
chr106253953962539641E070-12249
chr106253964762539920E070-11970
chr106253992762540021E070-11869
chr106254011262540265E070-11625
chr106254030862540358E070-11532
chr106253762562537684E071-14206
chr106253772662539398E071-12492
chr106253772662539398E073-12492
chr106253772662539398E074-12492
chr106253762562537684E081-14206
chr106253762562537684E082-14206
chr106253772662539398E082-12492
chr106253941562539475E082-12415
chr106253953962539641E082-12249
chr106253964762539920E082-11970
chr106253992762540021E082-11869
chr106254011262540265E082-11625
chr106254030862540358E082-11532