rs4685266

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0476 (14228/29888,GnomAD)
G=0496 (14463/29118,TOPMED)
G=0474 (2372/5008,1000G)
A==0406 (1564/3854,ALSPAC)
A==0409 (1517/3708,TWINSUK)

Position: chr3:15867259 (GRCh38.p7) (3p25.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 53 Enhancers around

Promoter: 18 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.15867259A>G
GRCh37.p13 chr 3	NC_000003.11:g.15908766A>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.638	G=0.362
1000Genomes	American	Sub	694	A=0.370	G=0.630
1000Genomes	East Asian	Sub	1008	A=0.673	G=0.327
1000Genomes	Europe	Sub	1006	A=0.404	G=0.596
1000Genomes	Global	Study-wide	5008	A=0.526	G=0.474
1000Genomes	South Asian	Sub	978	A=0.460	G=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.406	G=0.594
The Genome Aggregation Database	African	Sub	8690	A=0.604	G=0.396
The Genome Aggregation Database	American	Sub	836	A=0.350	G=0.650
The Genome Aggregation Database	East Asian	Sub	1614	A=0.704	G=0.296
The Genome Aggregation Database	Europe	Sub	18446	A=0.403	G=0.596
The Genome Aggregation Database	Global	Study-wide	29888	A=0.476	G=0.524
The Genome Aggregation Database	Other	Sub	302	A=0.390	G=0.610
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.503	G=0.496
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.409	G=0.591

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
rs4685266	0.000272	alcohol dependence	20201924

eQTL of rs4685266 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:15908766	EAF1	ENSG00000144597.9	A>G	2.7500e-26	439904	Cerebellum
Chr3:15908766	COLQ	ENSG00000206561.8	A>G	2.4569e-16	345508	Cerebellum
Chr3:15908766	AC090945.1	ENSG00000224728.1	A>G	7.5239e-6	-10788	Cerebellum
Chr3:15908766	EAF1	ENSG00000144597.9	A>G	8.3930e-25	439904	Cerebellar_Hemisphere
Chr3:15908766	COLQ	ENSG00000206561.8	A>G	1.6617e-14	345508	Cerebellar_Hemisphere
Chr3:15908766	AC090945.1	ENSG00000224728.1	A>G	1.0945e-3	-10788	Cerebellar_Hemisphere

meQTL of rs4685266 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	15863197	15863287	E067	-45479
chr3	15864794	15864853	E067	-43913
chr3	15898735	15898775	E067	-9991
chr3	15899314	15899427	E067	-9339
chr3	15899429	15899479	E067	-9287
chr3	15899506	15899556	E067	-9210
chr3	15944760	15945056	E067	35994
chr3	15862459	15862737	E068	-46029
chr3	15863197	15863287	E068	-45479
chr3	15887048	15887341	E068	-21425
chr3	15898735	15898775	E068	-9991
chr3	15899314	15899427	E068	-9339
chr3	15944760	15945056	E068	35994
chr3	15862459	15862737	E069	-46029
chr3	15863197	15863287	E069	-45479
chr3	15864794	15864853	E069	-43913
chr3	15898735	15898775	E069	-9991
chr3	15899314	15899427	E069	-9339
chr3	15899429	15899479	E069	-9287
chr3	15899506	15899556	E069	-9210
chr3	15898735	15898775	E070	-9991
chr3	15899314	15899427	E070	-9339
chr3	15899429	15899479	E070	-9287
chr3	15899506	15899556	E070	-9210
chr3	15902845	15902946	E070	-5820
chr3	15861146	15861464	E071	-47302
chr3	15862459	15862737	E071	-46029
chr3	15863197	15863287	E071	-45479
chr3	15864794	15864853	E071	-43913
chr3	15902845	15902946	E071	-5820
chr3	15944760	15945056	E071	35994
chr3	15863197	15863287	E072	-45479
chr3	15944760	15945056	E072	35994
chr3	15945315	15945644	E072	36549
chr3	15945741	15945931	E072	36975
chr3	15862459	15862737	E073	-46029
chr3	15863197	15863287	E073	-45479
chr3	15944760	15945056	E073	35994
chr3	15862459	15862737	E074	-46029
chr3	15863197	15863287	E074	-45479
chr3	15899314	15899427	E074	-9339
chr3	15899429	15899479	E074	-9287
chr3	15899506	15899556	E074	-9210
chr3	15902845	15902946	E074	-5820
chr3	15944760	15945056	E074	35994
chr3	15945315	15945644	E074	36549
chr3	15945741	15945931	E074	36975
chr3	15898735	15898775	E081	-9991
chr3	15899314	15899427	E081	-9339
chr3	15899429	15899479	E081	-9287
chr3	15899506	15899556	E081	-9210
chr3	15902845	15902946	E081	-5820
chr3	15898735	15898775	E082	-9991

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	15900237	15902498	E067	-6268
chr3	15902594	15902746	E067	-6020
chr3	15900237	15902498	E068	-6268
chr3	15902594	15902746	E068	-6020
chr3	15900237	15902498	E069	-6268
chr3	15902594	15902746	E069	-6020
chr3	15900237	15902498	E070	-6268
chr3	15900237	15902498	E071	-6268
chr3	15902594	15902746	E071	-6020
chr3	15900237	15902498	E072	-6268
chr3	15902594	15902746	E072	-6020
chr3	15900237	15902498	E073	-6268
chr3	15902594	15902746	E073	-6020
chr3	15900237	15902498	E074	-6268
chr3	15900237	15902498	E081	-6268
chr3	15902594	15902746	E081	-6020
chr3	15900237	15902498	E082	-6268
chr3	15902594	15902746	E082	-6020