rs17028719

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0048 (1446/29946,GnomAD)
G=0064 (1881/29118,TOPMED)
G=0113 (567/5008,1000G)
G=0006 (23/3854,ALSPAC)
G=0008 (31/3708,TWINSUK)

Position: chr1:5734948 (GRCh38.p7) (1p36.31)

Phenotype: AD | ND

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 68 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.5734948A>G
GRCh37.p13 chr 1	NC_000001.10:g.5795008A>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.849	G=0.151
1000Genomes	American	Sub	694	A=0.980	G=0.020
1000Genomes	East Asian	Sub	1008	A=0.871	G=0.129
1000Genomes	Europe	Sub	1006	A=0.992	G=0.008
1000Genomes	Global	Study-wide	5008	A=0.887	G=0.113
1000Genomes	South Asian	Sub	978	A=0.780	G=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.994	G=0.006
The Genome Aggregation Database	African	Sub	8722	A=0.874	G=0.126
The Genome Aggregation Database	American	Sub	838	A=0.990	G=0.010
The Genome Aggregation Database	East Asian	Sub	1618	A=0.870	G=0.130
The Genome Aggregation Database	Europe	Sub	18466	A=0.993	G=0.006
The Genome Aggregation Database	Global	Study-wide	29946	A=0.951	G=0.048
The Genome Aggregation Database	Other	Sub	302	A=0.980	G=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.935	G=0.064
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.992	G=0.008

PMID	Title	Author	Journal
22096494	A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.	Zuo L	PLoS One
22488850	Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.	Zuo L	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs17028719	0.00000089	alcohol dependence	22096494
rs17028719	0.0000032	alcohol and nictotine co-dependence	22488850

eQTL of rs17028719 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 rs17028719 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 )
chr1	5804944	5805051	E067	9936
chr1	5805128	5805294	E067	10120
chr1	5805332	5805428	E067	10324
chr1	5805891	5806162	E067	10883
chr1	5831742	5832033	E067	36734
chr1	5804517	5804745	E068	9509
chr1	5806195	5806406	E068	11187
chr1	5805891	5806162	E069	10883
chr1	5806195	5806406	E069	11187
chr1	5806778	5806990	E069	11770
chr1	5745812	5746100	E070	-48908
chr1	5769764	5769874	E070	-25134
chr1	5780662	5781649	E070	-13359
chr1	5785580	5785745	E070	-9263
chr1	5805891	5806162	E070	10883
chr1	5806195	5806406	E070	11187
chr1	5806778	5806990	E070	11770
chr1	5807031	5807081	E070	12023
chr1	5807339	5807761	E070	12331
chr1	5825594	5825684	E070	30586
chr1	5831100	5831618	E070	36092
chr1	5831742	5832033	E070	36734
chr1	5804944	5805051	E071	9936
chr1	5805891	5806162	E071	10883
chr1	5831100	5831618	E071	36092
chr1	5780662	5781649	E072	-13359
chr1	5806195	5806406	E072	11187
chr1	5816901	5817062	E072	21893
chr1	5817413	5817877	E072	22405
chr1	5805891	5806162	E073	10883
chr1	5806195	5806406	E073	11187
chr1	5804517	5804745	E074	9509
chr1	5804944	5805051	E074	9936
chr1	5805128	5805294	E074	10120
chr1	5805332	5805428	E074	10324
chr1	5805891	5806162	E074	10883
chr1	5806195	5806406	E074	11187
chr1	5831100	5831618	E074	36092
chr1	5748593	5748806	E081	-46202
chr1	5782840	5782890	E081	-12118
chr1	5783002	5783099	E081	-11909
chr1	5785580	5785745	E081	-9263
chr1	5803464	5803518	E081	8456
chr1	5804517	5804745	E081	9509
chr1	5804944	5805051	E081	9936
chr1	5805128	5805294	E081	10120
chr1	5805332	5805428	E081	10324
chr1	5805891	5806162	E081	10883
chr1	5806195	5806406	E081	11187
chr1	5806778	5806990	E081	11770
chr1	5807031	5807081	E081	12023
chr1	5807339	5807761	E081	12331
chr1	5812063	5812180	E081	17055
chr1	5812250	5812341	E081	17242
chr1	5812372	5812610	E081	17364
chr1	5816901	5817062	E081	21893
chr1	5817413	5817877	E081	22405
chr1	5825594	5825684	E081	30586
chr1	5831100	5831618	E081	36092
chr1	5783002	5783099	E082	-11909
chr1	5785580	5785745	E082	-9263
chr1	5806195	5806406	E082	11187
chr1	5806778	5806990	E082	11770
chr1	5807031	5807081	E082	12023
chr1	5807339	5807761	E082	12331
chr1	5816901	5817062	E082	21893
chr1	5817413	5817877	E082	22405
chr1	5831742	5832033	E082	36734