SNP Detail Info-rs12617579

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ALK : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

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)

Position: chr2:29266754 (GRCh38.p7) (2p23.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 48 Enhancers around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
ALK transcript variant 1	NM_004304.4:c.	N/A	Intron Variant
ALK transcript variant X1	XR_001738688.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.623	T=0.377
1000Genomes	American	Sub	694	C=0.200	T=0.800
1000Genomes	East Asian	Sub	1008	C=0.244	T=0.756
1000Genomes	Europe	Sub	1006	C=0.200	T=0.800
1000Genomes	Global	Study-wide	5008	C=0.327	T=0.673
1000Genomes	South Asian	Sub	978	C=0.240	T=0.760
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.191	T=0.809
The Genome Aggregation Database	African	Sub	8698	C=0.556	T=0.444
The Genome Aggregation Database	American	Sub	838	C=0.220	T=0.780
The Genome Aggregation Database	East Asian	Sub	1620	C=0.266	T=0.734
The Genome Aggregation Database	Europe	Sub	18480	C=0.178	T=0.821
The Genome Aggregation Database	Global	Study-wide	29938	C=0.294	T=0.705
The Genome Aggregation Database	Other	Sub	302	C=0.250	T=0.750
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.366	T=0.634
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.195	T=0.805

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

SNP ID	p-value	Traits	Study
rs12617579	3.81E-05	nicotine smoking	19268276

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	29446670	29447230	E067	-42390
chr2	29501950	29502182	E067	12330
chr2	29504472	29504736	E068	14852
chr2	29505746	29505826	E068	16126
chr2	29532054	29532398	E068	42434
chr2	29537268	29537318	E068	47648
chr2	29537361	29537456	E068	47741
chr2	29538604	29538731	E068	48984
chr2	29446670	29447230	E069	-42390
chr2	29446670	29447230	E070	-42390
chr2	29485434	29486131	E070	-3489
chr2	29490671	29490870	E070	1051
chr2	29490918	29490962	E070	1298
chr2	29491356	29491407	E070	1736
chr2	29492197	29492860	E070	2577
chr2	29493297	29493357	E070	3677
chr2	29493576	29493856	E070	3956
chr2	29494045	29494114	E070	4425
chr2	29501809	29501878	E070	12189
chr2	29501950	29502182	E070	12330
chr2	29502747	29502800	E070	13127
chr2	29505746	29505826	E070	16126
chr2	29513258	29513860	E070	23638
chr2	29527791	29527845	E070	38171
chr2	29532054	29532398	E070	42434
chr2	29537268	29537318	E070	47648
chr2	29537361	29537456	E070	47741
chr2	29532054	29532398	E071	42434
chr2	29538604	29538731	E071	48984
chr2	29504472	29504736	E072	14852
chr2	29537361	29537456	E072	47741
chr2	29446670	29447230	E073	-42390
chr2	29504472	29504736	E073	14852
chr2	29491356	29491407	E074	1736
chr2	29504472	29504736	E074	14852
chr2	29537268	29537318	E074	47648
chr2	29537361	29537456	E074	47741
chr2	29501809	29501878	E081	12189
chr2	29501950	29502182	E081	12330
chr2	29502747	29502800	E081	13127
chr2	29504472	29504736	E081	14852
chr2	29537268	29537318	E081	47648
chr2	29537361	29537456	E081	47741
chr2	29492197	29492860	E082	2577
chr2	29501809	29501878	E082	12189
chr2	29501950	29502182	E082	12330
chr2	29537268	29537318	E082	47648
chr2	29537361	29537456	E082	47741

rs12617579