SNP Detail Info-rs17049483

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC105373613 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0197 (5906/29950,GnomAD)
T=0194 (5674/29118,TOPMED)
T=0215 (1078/5008,1000G)
T=0200 (772/3854,ALSPAC)
T=0202 (748/3708,TWINSUK)

Position: chr2:129444413 (GRCh38.p7) (2q21.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 35 Enhancers around

Promoter: 1 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.129444413C>T
GRCh37.p13 chr 2	NC_000002.11:g.130201986C>T

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373613 transcript	XR_001739710.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.806	T=0.194
1000Genomes	American	Sub	694	C=0.740	T=0.260
1000Genomes	East Asian	Sub	1008	C=0.835	T=0.165
1000Genomes	Europe	Sub	1006	C=0.837	T=0.163
1000Genomes	Global	Study-wide	5008	C=0.785	T=0.215
1000Genomes	South Asian	Sub	978	C=0.680	T=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.800	T=0.200
The Genome Aggregation Database	African	Sub	8716	C=0.799	T=0.201
The Genome Aggregation Database	American	Sub	836	C=0.750	T=0.250
The Genome Aggregation Database	East Asian	Sub	1614	C=0.834	T=0.166
The Genome Aggregation Database	Europe	Sub	18484	C=0.803	T=0.196
The Genome Aggregation Database	Global	Study-wide	29950	C=0.802	T=0.197
The Genome Aggregation Database	Other	Sub	300	C=0.860	T=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.805	T=0.194
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.798	T=0.202

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

SNP ID	p-value	Traits	Study
rs17049483	0.0009	nicotine dependence	17158188

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	130197005	130197635	E070	-4351
chr2	130248271	130248515	E071	46285
chr2	130248798	130248888	E071	46812
chr2	130185920	130186058	E081	-15928
chr2	130194530	130194810	E081	-7176
chr2	130195124	130195211	E081	-6775
chr2	130195420	130195691	E081	-6295
chr2	130195925	130196610	E081	-5376
chr2	130197005	130197635	E081	-4351
chr2	130201651	130201724	E081	-262
chr2	130202067	130202132	E081	81
chr2	130227521	130227727	E081	25535
chr2	130236485	130237093	E081	34499
chr2	130237339	130237412	E081	35353
chr2	130237562	130237687	E081	35576
chr2	130248271	130248515	E081	46285
chr2	130248798	130248888	E081	46812
chr2	130250250	130250419	E081	48264
chr2	130154789	130155073	E082	-46913
chr2	130158519	130158674	E082	-43312
chr2	130158744	130158864	E082	-43122
chr2	130185920	130186058	E082	-15928
chr2	130194530	130194810	E082	-7176
chr2	130195124	130195211	E082	-6775
chr2	130195420	130195691	E082	-6295
chr2	130195925	130196610	E082	-5376
chr2	130197005	130197635	E082	-4351
chr2	130201651	130201724	E082	-262
chr2	130202067	130202132	E082	81
chr2	130227521	130227727	E082	25535
chr2	130236485	130237093	E082	34499
chr2	130237339	130237412	E082	35353
chr2	130237562	130237687	E082	35576
chr2	130248271	130248515	E082	46285
chr2	130250250	130250419	E082	48264

rs17049483