rs12664021

Homo sapiens
C>T
CDKAL1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0115 (3455/29904,GnomAD)
T=0109 (3186/29118,TOPMED)
T=0194 (972/5008,1000G)
T=0073 (282/3854,ALSPAC)
T=0079 (293/3708,TWINSUK)
chr6:20760849 (GRCh38.p7) (6p22.3)
ND
GWASdb2
1   publication(s)
See rs on genome
19 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.20760849C>T
GRCh37.p13 chr 6NC_000006.11:g.20761080C>T
CDKAL1 RefSeqGeneNG_021195.1:g.231393C>T

Gene: CDKAL1, CDK5 regulatory subunit associated protein 1 like 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDKAL1 transcriptNM_017774.3:c.N/AIntron Variant
CDKAL1 transcript variant X7XM_011514718.1:c.N/AIntron Variant
CDKAL1 transcript variant X8XM_011514719.2:c.N/AIntron Variant
CDKAL1 transcript variant X9XM_017010986.1:c.N/AIntron Variant
CDKAL1 transcript variant X12XM_017010987.1:c.N/AIntron Variant
CDKAL1 transcript variant X3XR_001743495.1:n.N/AIntron Variant
CDKAL1 transcript variant X4XR_001743496.1:n.N/AIntron Variant
CDKAL1 transcript variant X13XR_001743500.1:n.N/AIntron Variant
CDKAL1 transcript variant X14XR_001743501.1:n.N/AIntron Variant
CDKAL1 transcript variant X1XR_926265.1:n.N/AIntron Variant
CDKAL1 transcript variant X2XR_926266.1:n.N/AIntron Variant
CDKAL1 transcript variant X5XR_926267.1:n.N/AIntron Variant
CDKAL1 transcript variant X9XR_001743498.1:n.N/AGenic Upstream Transcript Variant
CDKAL1 transcript variant X10XR_001743499.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.835T=0.165
1000GenomesAmericanSub694C=0.850T=0.150
1000GenomesEast AsianSub1008C=0.663T=0.337
1000GenomesEuropeSub1006C=0.910T=0.090
1000GenomesGlobalStudy-wide5008C=0.806T=0.194
1000GenomesSouth AsianSub978C=0.770T=0.230
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.927T=0.073
The Genome Aggregation DatabaseAfricanSub8668C=0.863T=0.137
The Genome Aggregation DatabaseAmericanSub836C=0.860T=0.140
The Genome Aggregation DatabaseEast AsianSub1616C=0.655T=0.345
The Genome Aggregation DatabaseEuropeSub18482C=0.914T=0.085
The Genome Aggregation DatabaseGlobalStudy-wide29904C=0.884T=0.115
The Genome Aggregation DatabaseOtherSub302C=0.950T=0.050
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.890T=0.109
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.921T=0.079
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs126640210.00089nicotine smoking19268276

eQTL of rs12664021 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 rs12664021 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 )
chr62076356220763859E0672482
chr62077642720776484E06815347
chr62077655420776650E06815474
chr62079227420792577E06831194
chr62076356220763859E0692482
chr62077642720776484E06915347
chr62072517320725279E070-35801
chr62077642720776484E07015347
chr62077655420776650E07015474
chr62081040820810863E07049328
chr62076356220763859E0712482
chr62077642720776484E07115347
chr62077655420776650E07115474
chr62071924520719342E074-41738
chr62076356220763859E0742482
chr62072479620724954E081-36126
chr62072517320725279E081-35801
chr62072479620724954E082-36126
chr62072517320725279E082-35801