rs12617579

Homo sapiens
C>T
ALK : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0294 (8825/29938,GnomAD)
C==0366 (10656/29116,TOPMED)
C==0327 (1637/5008,1000G)
C==0191 (738/3854,ALSPAC)
C==0195 (724/3708,TWINSUK)
chr2:29266754 (GRCh38.p7) (2p23.2)
ND
GWASdb2
1   publication(s)
See rs on genome
48 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.29266754C>T
GRCh37.p13 chr 2NC_000002.11:g.29489620C>T
ALK RefSeqGene LRG_488

Gene: ALK, anaplastic lymphoma receptor tyrosine kinase(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ALK transcript variant 1NM_004304.4:c.N/AIntron Variant
ALK transcript variant X1XR_001738688.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.623T=0.377
1000GenomesAmericanSub694C=0.200T=0.800
1000GenomesEast AsianSub1008C=0.244T=0.756
1000GenomesEuropeSub1006C=0.200T=0.800
1000GenomesGlobalStudy-wide5008C=0.327T=0.673
1000GenomesSouth AsianSub978C=0.240T=0.760
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.191T=0.809
The Genome Aggregation DatabaseAfricanSub8698C=0.556T=0.444
The Genome Aggregation DatabaseAmericanSub838C=0.220T=0.780
The Genome Aggregation DatabaseEast AsianSub1620C=0.266T=0.734
The Genome Aggregation DatabaseEuropeSub18480C=0.178T=0.821
The Genome Aggregation DatabaseGlobalStudy-wide29938C=0.294T=0.705
The Genome Aggregation DatabaseOtherSub302C=0.250T=0.750
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.366T=0.634
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.195T=0.805
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
rs126175793.81E-05nicotine smoking19268276

eQTL of rs12617579 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 rs12617579 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 )
chr22944667029447230E067-42390
chr22950195029502182E06712330
chr22950447229504736E06814852
chr22950574629505826E06816126
chr22953205429532398E06842434
chr22953726829537318E06847648
chr22953736129537456E06847741
chr22953860429538731E06848984
chr22944667029447230E069-42390
chr22944667029447230E070-42390
chr22948543429486131E070-3489
chr22949067129490870E0701051
chr22949091829490962E0701298
chr22949135629491407E0701736
chr22949219729492860E0702577
chr22949329729493357E0703677
chr22949357629493856E0703956
chr22949404529494114E0704425
chr22950180929501878E07012189
chr22950195029502182E07012330
chr22950274729502800E07013127
chr22950574629505826E07016126
chr22951325829513860E07023638
chr22952779129527845E07038171
chr22953205429532398E07042434
chr22953726829537318E07047648
chr22953736129537456E07047741
chr22953205429532398E07142434
chr22953860429538731E07148984
chr22950447229504736E07214852
chr22953736129537456E07247741
chr22944667029447230E073-42390
chr22950447229504736E07314852
chr22949135629491407E0741736
chr22950447229504736E07414852
chr22953726829537318E07447648
chr22953736129537456E07447741
chr22950180929501878E08112189
chr22950195029502182E08112330
chr22950274729502800E08113127
chr22950447229504736E08114852
chr22953726829537318E08147648
chr22953736129537456E08147741
chr22949219729492860E0822577
chr22950180929501878E08212189
chr22950195029502182E08212330
chr22953726829537318E08247648
chr22953736129537456E08247741