SNP Detail Info-rs3218065

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CCNE1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0012 (1269/105168,ExAC)
A=0013 (406/29868,GnomAD)
A=0008 (249/29118,TOPMED)
G==0010 (140/13006,GO-ESP)
A=0005 (27/5008,1000G)
A=0013 (49/3854,ALSPAC)
A=0014 (53/3708,TWINSUK)

Position: chr19:29821675 (GRCh38.p7) (19q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 14 Enhancers around

Promoter: 30 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.29821675G>A
GRCh37.p13 chr 19	NC_000019.9:g.30312582G>A

Gene: CCNE1, cyclin E1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CCNE1 transcript variant 1	NM_001238.3:c.	N/A	Intron Variant
CCNE1 transcript variant 3	NM_001322259.1:c.	N/A	Intron Variant
CCNE1 transcript variant 4	NM_001322261.1:c.	N/A	Intron Variant
CCNE1 transcript variant 5	NM_001322262.1:c.	N/A	Intron Variant
CCNE1 transcript variant X1	XM_011527440.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=1.000	A=0.000
1000Genomes	American	Sub	694	G=0.990	A=0.010
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.978	A=0.022
1000Genomes	Global	Study-wide	5008	G=0.995	A=0.005
1000Genomes	South Asian	Sub	978	G=1.000	A=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.987	A=0.013
The Exome Aggregation Consortium	American	Sub	19406	G=0.994	A=0.006
The Exome Aggregation Consortium	Asian	Sub	21942	G=0.999	A=0.000
The Exome Aggregation Consortium	Europe	Sub	62998	G=0.982	A=0.018
The Exome Aggregation Consortium	Global	Study-wide	105168	G=0.987	A=0.012
The Exome Aggregation Consortium	Other	Sub	822	G=0.990	A=0.010
The Genome Aggregation Database	African	Sub	8694	G=0.997	A=0.003
The Genome Aggregation Database	American	Sub	836	G=0.990	A=0.010
The Genome Aggregation Database	East Asian	Sub	1618	G=1.000	A=0.000
The Genome Aggregation Database	Europe	Sub	18418	G=0.979	A=0.020
The Genome Aggregation Database	Global	Study-wide	29868	G=0.986	A=0.013
The Genome Aggregation Database	Other	Sub	302	G=1.000	A=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.991	A=0.008
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.986	A=0.014

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
rs3218065	0.00025	alcohol dependence	20201924

eQTL of rs3218065 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 rs3218065 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr19	30289737	30290141	E081	-22441
chr19	30290145	30290266	E081	-22316
chr19	30346083	30346345	E081	33501
chr19	30346444	30346494	E081	33862
chr19	30346566	30347135	E081	33984
chr19	30347198	30347323	E081	34616
chr19	30347384	30347490	E081	34802
chr19	30347520	30347628	E081	34938
chr19	30346083	30346345	E082	33501
chr19	30346444	30346494	E082	33862
chr19	30346566	30347135	E082	33984
chr19	30347198	30347323	E082	34616
chr19	30347384	30347490	E082	34802
chr19	30347520	30347628	E082	34938

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	30333562	30337258	E067	20980
chr19	30301140	30303143	E068	-9439
chr19	30303266	30303331	E068	-9251
chr19	30303398	30304238	E068	-8344
chr19	30333562	30337258	E068	20980
chr19	30301140	30303143	E069	-9439
chr19	30303266	30303331	E069	-9251
chr19	30303398	30304238	E069	-8344
chr19	30333562	30337258	E069	20980
chr19	30301140	30303143	E070	-9439
chr19	30303266	30303331	E070	-9251
chr19	30333562	30337258	E070	20980
chr19	30301140	30303143	E071	-9439
chr19	30303266	30303331	E071	-9251
chr19	30303398	30304238	E071	-8344
chr19	30333562	30337258	E071	20980
chr19	30301140	30303143	E072	-9439
chr19	30303266	30303331	E072	-9251
chr19	30303398	30304238	E072	-8344
chr19	30333562	30337258	E072	20980
chr19	30301140	30303143	E073	-9439
chr19	30303266	30303331	E073	-9251
chr19	30303398	30304238	E073	-8344
chr19	30333562	30337258	E073	20980
chr19	30301140	30303143	E074	-9439
chr19	30333562	30337258	E074	20980
chr19	30301140	30303143	E082	-9439
chr19	30303266	30303331	E082	-9251
chr19	30303398	30304238	E082	-8344
chr19	30333562	30337258	E082	20980

rs3218065