rs11056079

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

SLC2A14 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0496 (14826/29860,GnomAD)
T=0479 (2399/5008,1000G)
C==0498 (1921/3854,ALSPAC)
T=0485 (1800/3708,TWINSUK)

Position: chr12:7844294 (GRCh38.p7) (12p13.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 5 Enhancers around

Promoter: 3 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.7844294C>T
GRCh37.p13 chr 12	NC_000012.11:g.7996890C>T

Gene: SLC2A14, solute carrier family 2 member 14(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC2A14 transcript variant 1	NM_001286233.1:c.	N/A	Intron Variant
SLC2A14 transcript variant 3	NM_001286234.1:c.	N/A	Intron Variant
SLC2A14 transcript variant 4	NM_001286235.1:c.	N/A	Intron Variant
SLC2A14 transcript variant 5	NM_001286236.1:c.	N/A	Intron Variant
SLC2A14 transcript variant 6	NM_001286237.1:c.	N/A	Intron Variant
SLC2A14 transcript variant 2	NM_153449.3:c.	N/A	Intron Variant
SLC2A14 transcript variant X8	XM_005253315.3:c.	N/A	Intron Variant
SLC2A14 transcript variant X9	XM_005253317.4:c.	N/A	Intron Variant
SLC2A14 transcript variant X5	XM_011520562.1:c.	N/A	Intron Variant
SLC2A14 transcript variant X11	XM_011520563.2:c.	N/A	Intron Variant
SLC2A14 transcript variant X12	XM_011520564.2:c.	N/A	Intron Variant
SLC2A14 transcript variant X13	XM_011520565.2:c.	N/A	Intron Variant
SLC2A14 transcript variant X1	XM_017018841.1:c.	N/A	Intron Variant
SLC2A14 transcript variant X2	XM_017018842.1:c.	N/A	Intron Variant
SLC2A14 transcript variant X3	XM_017018843.1:c.	N/A	Intron Variant
SLC2A14 transcript variant X3	XM_017018844.1:c.	N/A	Intron Variant
SLC2A14 transcript variant X5	XM_017018845.1:c.	N/A	Intron Variant
SLC2A14 transcript variant X6	XM_017018846.1:c.	N/A	Intron Variant
SLC2A14 transcript variant X9	XM_017018847.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.440	T=0.560
1000Genomes	American	Sub	694	C=0.650	T=0.350
1000Genomes	East Asian	Sub	1008	C=0.583	T=0.417
1000Genomes	Europe	Sub	1006	C=0.457	T=0.543
1000Genomes	Global	Study-wide	5008	C=0.521	T=0.479
1000Genomes	South Asian	Sub	978	C=0.540	T=0.460
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.498	T=0.502
The Genome Aggregation Database	African	Sub	8682	C=0.447	T=0.553
The Genome Aggregation Database	American	Sub	834	C=0.680	T=0.320
The Genome Aggregation Database	East Asian	Sub	1600	C=0.581	T=0.419
The Genome Aggregation Database	Europe	Sub	18442	C=0.517	T=0.482
The Genome Aggregation Database	Global	Study-wide	29860	C=0.503	T=0.496
The Genome Aggregation Database	Other	Sub	302	C=0.370	T=0.630
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.515	T=0.485

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
rs11056079	0.00066	alcohol dependence(early age of onset)	20201924
rs11056079	0.00071	alcohol dependence	20201924

eQTL of rs11056079 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 rs11056079 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 )
chr12	7991285	7991345	E081	-5545
chr12	7992293	7992396	E081	-4494
chr12	7992411	7992517	E081	-4373
chr12	7992629	7992686	E081	-4204
chr12	7992808	7992858	E081	-4032

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	8025080	8025343	E068	28190
chr12	8025366	8025563	E068	28476
chr12	8025366	8025563	E071	28476