rs4688470

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0292 (8736/29922,GnomAD)
A==0349 (10185/29118,TOPMED)
A==0333 (1667/5008,1000G)
A==0103 (398/3854,ALSPAC)
A==0112 (415/3708,TWINSUK)

Position: chr3:64511675 (GRCh38.p7) (3p14.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 97 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.64511675A>C
GRCh37.p13 chr 3	NC_000003.11:g.64497351A>C
RNU6-739P pseudogene	NG_042944.1:g.21A>C

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.707	C=0.293
1000Genomes	American	Sub	694	A=0.120	C=0.880
1000Genomes	East Asian	Sub	1008	A=0.331	C=0.669
1000Genomes	Europe	Sub	1006	A=0.127	C=0.873
1000Genomes	Global	Study-wide	5008	A=0.333	C=0.667
1000Genomes	South Asian	Sub	978	A=0.190	C=0.810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.103	C=0.897
The Genome Aggregation Database	African	Sub	8684	A=0.626	C=0.374
The Genome Aggregation Database	American	Sub	836	A=0.090	C=0.910
The Genome Aggregation Database	East Asian	Sub	1612	A=0.339	C=0.661
The Genome Aggregation Database	Europe	Sub	18488	A=0.143	C=0.857
The Genome Aggregation Database	Global	Study-wide	29922	A=0.292	C=0.708
The Genome Aggregation Database	Other	Sub	302	A=0.100	C=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.349	C=0.650
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.112	C=0.888

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs4688470	0.000504	alcohol dependence	20201924

eQTL of rs4688470 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 rs4688470 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 )
chr3	64449309	64449461	E067	-47890
chr3	64533695	64533823	E067	36344
chr3	64533845	64534526	E067	36494
chr3	64449309	64449461	E068	-47890
chr3	64469907	64470555	E068	-26796
chr3	64474578	64474635	E068	-22716
chr3	64474721	64474832	E068	-22519
chr3	64490941	64491028	E068	-6323
chr3	64491097	64491448	E068	-5903
chr3	64519232	64519910	E068	21881
chr3	64533695	64533823	E068	36344
chr3	64533845	64534526	E068	36494
chr3	64534534	64534673	E068	37183
chr3	64449309	64449461	E069	-47890
chr3	64474578	64474635	E069	-22716
chr3	64474721	64474832	E069	-22519
chr3	64519232	64519910	E069	21881
chr3	64533695	64533823	E069	36344
chr3	64533845	64534526	E069	36494
chr3	64534534	64534673	E069	37183
chr3	64447793	64447870	E070	-49481
chr3	64447936	64448516	E070	-48835
chr3	64448584	64448868	E070	-48483
chr3	64449309	64449461	E070	-47890
chr3	64450704	64450906	E070	-46445
chr3	64451109	64451173	E070	-46178
chr3	64474578	64474635	E070	-22716
chr3	64474721	64474832	E070	-22519
chr3	64474887	64475673	E070	-21678
chr3	64491097	64491448	E070	-5903
chr3	64491516	64491599	E070	-5752
chr3	64532380	64532430	E070	35029
chr3	64532452	64532571	E070	35101
chr3	64532682	64532726	E070	35331
chr3	64532877	64533122	E070	35526
chr3	64533463	64533507	E070	36112
chr3	64533695	64533823	E070	36344
chr3	64533845	64534526	E070	36494
chr3	64534534	64534673	E070	37183
chr3	64535270	64535320	E070	37919
chr3	64535687	64535737	E070	38336
chr3	64540343	64540448	E070	42992
chr3	64447793	64447870	E071	-49481
chr3	64449309	64449461	E071	-47890
chr3	64469907	64470555	E071	-26796
chr3	64474721	64474832	E071	-22519
chr3	64474887	64475673	E071	-21678
chr3	64491097	64491448	E071	-5903
chr3	64519232	64519910	E071	21881
chr3	64519964	64520018	E071	22613
chr3	64533695	64533823	E071	36344
chr3	64533845	64534526	E071	36494
chr3	64534534	64534673	E071	37183
chr3	64447936	64448516	E072	-48835
chr3	64448584	64448868	E072	-48483
chr3	64449309	64449461	E072	-47890
chr3	64469907	64470555	E072	-26796
chr3	64519232	64519910	E072	21881
chr3	64533695	64533823	E072	36344
chr3	64533845	64534526	E072	36494
chr3	64534534	64534673	E072	37183
chr3	64519232	64519910	E073	21881
chr3	64519964	64520018	E073	22613
chr3	64533695	64533823	E073	36344
chr3	64533845	64534526	E073	36494
chr3	64449309	64449461	E074	-47890
chr3	64469907	64470555	E074	-26796
chr3	64474578	64474635	E074	-22716
chr3	64474721	64474832	E074	-22519
chr3	64515806	64516186	E074	18455
chr3	64516226	64516411	E074	18875
chr3	64516507	64516558	E074	19156
chr3	64519232	64519910	E074	21881
chr3	64519964	64520018	E074	22613
chr3	64533845	64534526	E074	36494
chr3	64468776	64468826	E081	-28525
chr3	64469055	64469277	E081	-28074
chr3	64469376	64469426	E081	-27925
chr3	64474578	64474635	E081	-22716
chr3	64474721	64474832	E081	-22519
chr3	64474887	64475673	E081	-21678
chr3	64480196	64480521	E081	-16830
chr3	64480688	64480768	E081	-16583
chr3	64519964	64520018	E081	22613
chr3	64533695	64533823	E081	36344
chr3	64533845	64534526	E081	36494
chr3	64534534	64534673	E081	37183
chr3	64535270	64535320	E081	37919
chr3	64540343	64540448	E081	42992
chr3	64474721	64474832	E082	-22519
chr3	64474887	64475673	E082	-21678
chr3	64480196	64480521	E082	-16830
chr3	64480688	64480768	E082	-16583
chr3	64519964	64520018	E082	22613
chr3	64525103	64525691	E082	27752
chr3	64533845	64534526	E082	36494
chr3	64534534	64534673	E082	37183