rs17040470

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0089 (2664/29944,GnomAD)
A=0072 (2104/29118,TOPMED)
A=0145 (724/5008,1000G)
A=0062 (238/3854,ALSPAC)
A=0058 (216/3708,TWINSUK)

Position: chr12:108409978 (GRCh38.p7) (12q23.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 74 Enhancers around

Promoter: 1 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.108409978G>A
GRCh37.p13 chr 12	NC_000012.11:g.108803755G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.943	A=0.057
1000Genomes	American	Sub	694	G=0.920	A=0.080
1000Genomes	East Asian	Sub	1008	G=0.618	A=0.382
1000Genomes	Europe	Sub	1006	G=0.907	A=0.093
1000Genomes	Global	Study-wide	5008	G=0.855	A=0.145
1000Genomes	South Asian	Sub	978	G=0.880	A=0.120
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.938	A=0.062
The Genome Aggregation Database	African	Sub	8724	G=0.946	A=0.054
The Genome Aggregation Database	American	Sub	838	G=0.930	A=0.070
The Genome Aggregation Database	East Asian	Sub	1602	G=0.598	A=0.402
The Genome Aggregation Database	Europe	Sub	18482	G=0.921	A=0.078
The Genome Aggregation Database	Global	Study-wide	29944	G=0.911	A=0.089
The Genome Aggregation Database	Other	Sub	298	G=0.890	A=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.927	A=0.072
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.942	A=0.058

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
rs17040470	0.000155	alcohol dependence	20201924

eQTL of rs17040470 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 rs17040470 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	108792846	108792909	E067	-10846
chr12	108793164	108793244	E067	-10511
chr12	108793302	108793564	E067	-10191
chr12	108793571	108793686	E067	-10069
chr12	108793302	108793564	E068	-10191
chr12	108793571	108793686	E068	-10069
chr12	108793884	108794031	E068	-9724
chr12	108794290	108794526	E068	-9229
chr12	108792496	108792546	E069	-11209
chr12	108792846	108792909	E069	-10846
chr12	108793884	108794031	E069	-9724
chr12	108784493	108785071	E070	-18684
chr12	108787678	108787770	E070	-15985
chr12	108787975	108788517	E070	-15238
chr12	108788582	108788879	E070	-14876
chr12	108792846	108792909	E070	-10846
chr12	108793164	108793244	E070	-10511
chr12	108793884	108794031	E070	-9724
chr12	108794290	108794526	E070	-9229
chr12	108794648	108794706	E070	-9049
chr12	108795022	108795088	E070	-8667
chr12	108795847	108795973	E070	-7782
chr12	108801648	108801785	E070	-1970
chr12	108802295	108802345	E070	-1410
chr12	108803020	108803082	E070	-673
chr12	108803182	108803710	E070	-45
chr12	108804336	108804420	E070	581
chr12	108805097	108805182	E070	1342
chr12	108805584	108805640	E070	1829
chr12	108808705	108808770	E070	4950
chr12	108835235	108835772	E070	31480
chr12	108835782	108836370	E070	32027
chr12	108840538	108840898	E070	36783
chr12	108840933	108841666	E070	37178
chr12	108841837	108841953	E070	38082
chr12	108842098	108842243	E070	38343
chr12	108793164	108793244	E071	-10511
chr12	108793302	108793564	E071	-10191
chr12	108793571	108793686	E071	-10069
chr12	108793164	108793244	E072	-10511
chr12	108793302	108793564	E072	-10191
chr12	108793164	108793244	E073	-10511
chr12	108793302	108793564	E073	-10191
chr12	108793571	108793686	E073	-10069
chr12	108840933	108841666	E073	37178
chr12	108793164	108793244	E074	-10511
chr12	108793302	108793564	E074	-10191
chr12	108793571	108793686	E074	-10069
chr12	108793884	108794031	E074	-9724
chr12	108787975	108788517	E081	-15238
chr12	108788582	108788879	E081	-14876
chr12	108793164	108793244	E081	-10511
chr12	108793302	108793564	E081	-10191
chr12	108793571	108793686	E081	-10069
chr12	108793884	108794031	E081	-9724
chr12	108794290	108794526	E081	-9229
chr12	108794648	108794706	E081	-9049
chr12	108804336	108804420	E081	581
chr12	108805097	108805182	E081	1342
chr12	108840183	108840531	E081	36428
chr12	108840538	108840898	E081	36783
chr12	108787325	108787369	E082	-16386
chr12	108787678	108787770	E082	-15985
chr12	108787975	108788517	E082	-15238
chr12	108788582	108788879	E082	-14876
chr12	108792846	108792909	E082	-10846
chr12	108793164	108793244	E082	-10511
chr12	108793302	108793564	E082	-10191
chr12	108793571	108793686	E082	-10069
chr12	108793884	108794031	E082	-9724
chr12	108794290	108794526	E082	-9229
chr12	108852677	108852742	E082	48922
chr12	108852898	108852950	E082	49143
chr12	108852981	108853262	E082	49226

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	108822642	108822738	E081	18887