rs7749709

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC101928277 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0497 (14896/29924,GnomAD)
G==0469 (13681/29118,TOPMED)
G==0455 (2280/5008,1000G)
A=0468 (1805/3854,ALSPAC)
A=0458 (1697/3708,TWINSUK)

Position: chr6:134758479 (GRCh38.p7) (6q23.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 121 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.134758479G>A
GRCh37.p13 chr 6	NC_000006.11:g.135079617G>A

Gene: LOC101928277, uncharacterized LOC101928277(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC101928277 transcript variant X1	XR_001744363.1:n.	N/A	Intron Variant
LOC101928277 transcript variant X2	XR_001744364.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.377	A=0.623
1000Genomes	American	Sub	694	G=0.420	A=0.580
1000Genomes	East Asian	Sub	1008	G=0.403	A=0.597
1000Genomes	Europe	Sub	1006	G=0.552	A=0.448
1000Genomes	Global	Study-wide	5008	G=0.455	A=0.545
1000Genomes	South Asian	Sub	978	G=0.540	A=0.460
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.532	A=0.468
The Genome Aggregation Database	African	Sub	8698	G=0.398	A=0.602
The Genome Aggregation Database	American	Sub	838	G=0.410	A=0.590
The Genome Aggregation Database	East Asian	Sub	1612	G=0.370	A=0.630
The Genome Aggregation Database	Europe	Sub	18474	G=0.558	A=0.441
The Genome Aggregation Database	Global	Study-wide	29924	G=0.497	A=0.502
The Genome Aggregation Database	Other	Sub	302	G=0.590	A=0.410
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.469	A=0.530
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.542	A=0.458

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

P-Value

SNP ID	p-value	Traits	Study
rs7749709	1.16E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs7749709 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 rs7749709 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 )
chr6	135030220	135030488	E067	-49129
chr6	135040751	135040849	E067	-38768
chr6	135041031	135041106	E067	-38511
chr6	135041129	135041344	E067	-38273
chr6	135041430	135042409	E067	-37208
chr6	135043331	135043409	E067	-36208
chr6	135043468	135043607	E067	-36010
chr6	135043629	135044604	E067	-35013
chr6	135044656	135044936	E067	-34681
chr6	135044996	135045134	E067	-34483
chr6	135045207	135045290	E067	-34327
chr6	135045305	135045405	E067	-34212
chr6	135061458	135062096	E067	-17521
chr6	135062158	135062248	E067	-17369
chr6	135062375	135062543	E067	-17074
chr6	135062748	135062802	E067	-16815
chr6	135116954	135117109	E067	37337
chr6	135127748	135127818	E067	48131
chr6	135041031	135041106	E068	-38511
chr6	135041129	135041344	E068	-38273
chr6	135041430	135042409	E068	-37208
chr6	135042589	135042665	E068	-36952
chr6	135043629	135044604	E068	-35013
chr6	135044656	135044936	E068	-34681
chr6	135044996	135045134	E068	-34483
chr6	135045207	135045290	E068	-34327
chr6	135045305	135045405	E068	-34212
chr6	135045666	135045802	E068	-33815
chr6	135052394	135052545	E068	-27072
chr6	135061458	135062096	E068	-17521
chr6	135062158	135062248	E068	-17369
chr6	135062375	135062543	E068	-17074
chr6	135062748	135062802	E068	-16815
chr6	135037157	135037232	E069	-42385
chr6	135040409	135040453	E069	-39164
chr6	135040751	135040849	E069	-38768
chr6	135041031	135041106	E069	-38511
chr6	135041129	135041344	E069	-38273
chr6	135041430	135042409	E069	-37208
chr6	135043468	135043607	E069	-36010
chr6	135043629	135044604	E069	-35013
chr6	135044656	135044936	E069	-34681
chr6	135044996	135045134	E069	-34483
chr6	135045207	135045290	E069	-34327
chr6	135045305	135045405	E069	-34212
chr6	135046656	135046784	E069	-32833
chr6	135046821	135047145	E069	-32472
chr6	135050571	135050690	E069	-28927
chr6	135050862	135050976	E069	-28641
chr6	135050983	135051101	E069	-28516
chr6	135051148	135051430	E069	-28187
chr6	135062158	135062248	E069	-17369
chr6	135062375	135062543	E069	-17074
chr6	135062748	135062802	E069	-16815
chr6	135116954	135117109	E069	37337
chr6	135050571	135050690	E070	-28927
chr6	135050862	135050976	E070	-28641
chr6	135050983	135051101	E070	-28516
chr6	135051148	135051430	E070	-28187
chr6	135030220	135030488	E071	-49129
chr6	135037157	135037232	E071	-42385
chr6	135041031	135041106	E071	-38511
chr6	135041129	135041344	E071	-38273
chr6	135041430	135042409	E071	-37208
chr6	135043629	135044604	E071	-35013
chr6	135044656	135044936	E071	-34681
chr6	135044996	135045134	E071	-34483
chr6	135045207	135045290	E071	-34327
chr6	135045305	135045405	E071	-34212
chr6	135045666	135045802	E071	-33815
chr6	135045867	135046477	E071	-33140
chr6	135046656	135046784	E071	-32833
chr6	135046821	135047145	E071	-32472
chr6	135061458	135062096	E071	-17521
chr6	135116954	135117109	E071	37337
chr6	135127748	135127818	E071	48131
chr6	135041031	135041106	E072	-38511
chr6	135041129	135041344	E072	-38273
chr6	135041430	135042409	E072	-37208
chr6	135043629	135044604	E072	-35013
chr6	135046821	135047145	E072	-32472
chr6	135050983	135051101	E072	-28516
chr6	135051148	135051430	E072	-28187
chr6	135061458	135062096	E072	-17521
chr6	135062158	135062248	E072	-17369
chr6	135127748	135127818	E072	48131
chr6	135040751	135040849	E073	-38768
chr6	135041031	135041106	E073	-38511
chr6	135041129	135041344	E073	-38273
chr6	135041430	135042409	E073	-37208
chr6	135046656	135046784	E073	-32833
chr6	135046821	135047145	E073	-32472
chr6	135030220	135030488	E074	-49129
chr6	135040409	135040453	E074	-39164
chr6	135041430	135042409	E074	-37208
chr6	135044656	135044936	E074	-34681
chr6	135044996	135045134	E074	-34483
chr6	135045207	135045290	E074	-34327
chr6	135045305	135045405	E074	-34212
chr6	135045867	135046477	E074	-33140
chr6	135046656	135046784	E074	-32833
chr6	135127748	135127818	E074	48131
chr6	135050571	135050690	E081	-28927
chr6	135050862	135050976	E081	-28641
chr6	135050983	135051101	E081	-28516
chr6	135051148	135051430	E081	-28187
chr6	135051525	135051607	E081	-28010
chr6	135051820	135052112	E081	-27505
chr6	135062158	135062248	E081	-17369
chr6	135062375	135062543	E081	-17074
chr6	135062748	135062802	E081	-16815
chr6	135063004	135063149	E081	-16468
chr6	135041031	135041106	E082	-38511
chr6	135041129	135041344	E082	-38273
chr6	135050571	135050690	E082	-28927
chr6	135050862	135050976	E082	-28641
chr6	135060764	135061442	E082	-18175
chr6	135061458	135062096	E082	-17521
chr6	135062158	135062248	E082	-17369
chr6	135062375	135062543	E082	-17074
chr6	135062748	135062802	E082	-16815