SNP Detail Info-rs11683474

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

LOC107985955 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0107 (3224/29880,GnomAD)
T=0097 (2840/29118,TOPMED)
T=0049 (244/5008,1000G)
T=0153 (589/3854,ALSPAC)
T=0149 (551/3708,TWINSUK)

Position: chr2:156816316 (GRCh38.p7) (2q24.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 16 Enhancers around

Promoter: 19 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.156816316A>T
GRCh37.p13 chr 2	NC_000002.11:g.157672828A>T

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985955 transcript variant X1	XR_001739753.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.980	T=0.020
1000Genomes	American	Sub	694	A=0.940	T=0.060
1000Genomes	East Asian	Sub	1008	A=1.000	T=0.000
1000Genomes	Europe	Sub	1006	A=0.860	T=0.140
1000Genomes	Global	Study-wide	5008	A=0.951	T=0.049
1000Genomes	South Asian	Sub	978	A=0.960	T=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.847	T=0.153
The Genome Aggregation Database	African	Sub	8722	A=0.960	T=0.040
The Genome Aggregation Database	American	Sub	838	A=0.930	T=0.070
The Genome Aggregation Database	East Asian	Sub	1616	A=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18402	A=0.848	T=0.151
The Genome Aggregation Database	Global	Study-wide	29880	A=0.892	T=0.107
The Genome Aggregation Database	Other	Sub	302	A=0.910	T=0.090
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.902	T=0.097
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.851	T=0.149

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

SNP ID	p-value	Traits	Study
rs11683474	0.00000151	Nicotine dependence (smoking)	20158304
rs11683474	0.000002	Comorbid alcohol and nicotine dependence	20158304

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	157640418	157640475	E070	-32353
chr2	157640544	157641150	E070	-31678
chr2	157656308	157656380	E071	-16448
chr2	157640418	157640475	E081	-32353
chr2	157640544	157641150	E081	-31678
chr2	157657424	157657533	E081	-15295
chr2	157657613	157657770	E081	-15058
chr2	157657838	157657903	E081	-14925
chr2	157659595	157659645	E081	-13183
chr2	157659782	157660085	E081	-12743
chr2	157720830	157721630	E081	48002
chr2	157722444	157722500	E081	49616
chr2	157640418	157640475	E082	-32353
chr2	157640544	157641150	E082	-31678
chr2	157657838	157657903	E082	-14925
chr2	157720830	157721630	E082	48002

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	157656619	157657092	E067	-15736
chr2	157657155	157657251	E067	-15577
chr2	157656619	157657092	E068	-15736
chr2	157657155	157657251	E068	-15577
chr2	157656619	157657092	E069	-15736
chr2	157657155	157657251	E069	-15577
chr2	157656619	157657092	E070	-15736
chr2	157657155	157657251	E070	-15577
chr2	157656619	157657092	E071	-15736
chr2	157657155	157657251	E071	-15577
chr2	157656619	157657092	E072	-15736
chr2	157657155	157657251	E072	-15577
chr2	157656619	157657092	E073	-15736
chr2	157657155	157657251	E073	-15577
chr2	157656619	157657092	E074	-15736
chr2	157657155	157657251	E074	-15577
chr2	157657155	157657251	E081	-15577
chr2	157656619	157657092	E082	-15736
chr2	157657155	157657251	E082	-15577

rs11683474