rs1345479

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

VPS54 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0218 (6534/29948,GnomAD)
G=0174 (5069/29116,TOPMED)
G=0128 (640/5008,1000G)
G=0246 (950/3854,ALSPAC)
G=0252 (936/3708,TWINSUK)

Position: chr2:63903097 (GRCh38.p7) (2p14)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 139 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.63903097A>G
GRCh37.p13 chr 2	NC_000002.11:g.64130231A>G
VPS54 RefSeqGene	NG_042277.1:g.120984T>C

Gene: VPS54, VPS54, GARP complex subunit(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
VPS54 transcript variant 2	NM_001005739.1:c.	N/A	Intron Variant
VPS54 transcript variant 1	NM_016516.2:c.	N/A	Intron Variant
VPS54 transcript variant X1	XM_006712029.3:c.	N/A	Intron Variant
VPS54 transcript variant X1	XM_017004316.1:c.	N/A	Intron Variant
VPS54 transcript variant X4	XR_001738770.1:n.	N/A	Intron Variant
VPS54 transcript variant X3	XR_244939.4:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.895	G=0.105
1000Genomes	American	Sub	694	A=0.790	G=0.210
1000Genomes	East Asian	Sub	1008	A=0.928	G=0.072
1000Genomes	Europe	Sub	1006	A=0.793	G=0.207
1000Genomes	Global	Study-wide	5008	A=0.872	G=0.128
1000Genomes	South Asian	Sub	978	A=0.930	G=0.070
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.754	G=0.246
The Genome Aggregation Database	African	Sub	8716	A=0.876	G=0.124
The Genome Aggregation Database	American	Sub	836	A=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1618	A=0.927	G=0.073
The Genome Aggregation Database	Europe	Sub	18476	A=0.721	G=0.278
The Genome Aggregation Database	Global	Study-wide	29948	A=0.781	G=0.218
The Genome Aggregation Database	Other	Sub	302	A=0.880	G=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.825	G=0.174
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.748	G=0.252

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
rs1345479	0.00099	alcohol dependence	20201924

eQTL of rs1345479 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 rs1345479 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 )
chr2	64080516	64080702	E067	-49529
chr2	64080727	64080887	E067	-49344
chr2	64080896	64080975	E067	-49256
chr2	64081019	64081300	E067	-48931
chr2	64081399	64081580	E067	-48651
chr2	64081622	64081718	E067	-48513
chr2	64081786	64081902	E067	-48329
chr2	64081918	64081983	E067	-48248
chr2	64082014	64082140	E067	-48091
chr2	64082197	64082237	E067	-47994
chr2	64096942	64097025	E067	-33206
chr2	64101547	64101822	E067	-28409
chr2	64101951	64102964	E067	-27267
chr2	64103000	64103369	E067	-26862
chr2	64118923	64119039	E067	-11192
chr2	64080516	64080702	E068	-49529
chr2	64080727	64080887	E068	-49344
chr2	64080896	64080975	E068	-49256
chr2	64081019	64081300	E068	-48931
chr2	64081399	64081580	E068	-48651
chr2	64081622	64081718	E068	-48513
chr2	64081786	64081902	E068	-48329
chr2	64081918	64081983	E068	-48248
chr2	64082014	64082140	E068	-48091
chr2	64082197	64082237	E068	-47994
chr2	64096942	64097025	E068	-33206
chr2	64097961	64098068	E068	-32163
chr2	64098298	64098481	E068	-31750
chr2	64098531	64098599	E068	-31632
chr2	64101547	64101822	E068	-28409
chr2	64101951	64102964	E068	-27267
chr2	64103000	64103369	E068	-26862
chr2	64103606	64103732	E068	-26499
chr2	64103778	64104022	E068	-26209
chr2	64107709	64108197	E068	-22034
chr2	64108399	64108563	E068	-21668
chr2	64118923	64119039	E068	-11192
chr2	64080516	64080702	E069	-49529
chr2	64080727	64080887	E069	-49344
chr2	64080896	64080975	E069	-49256
chr2	64081019	64081300	E069	-48931
chr2	64081399	64081580	E069	-48651
chr2	64081622	64081718	E069	-48513
chr2	64081786	64081902	E069	-48329
chr2	64081918	64081983	E069	-48248
chr2	64082014	64082140	E069	-48091
chr2	64082197	64082237	E069	-47994
chr2	64100349	64100399	E069	-29832
chr2	64101547	64101822	E069	-28409
chr2	64101951	64102964	E069	-27267
chr2	64103000	64103369	E069	-26862
chr2	64081019	64081300	E071	-48931
chr2	64081399	64081580	E071	-48651
chr2	64081622	64081718	E071	-48513
chr2	64081786	64081902	E071	-48329
chr2	64081918	64081983	E071	-48248
chr2	64082014	64082140	E071	-48091
chr2	64082197	64082237	E071	-47994
chr2	64082442	64082520	E071	-47711
chr2	64082567	64082640	E071	-47591
chr2	64082713	64082901	E071	-47330
chr2	64082922	64082973	E071	-47258
chr2	64088337	64088701	E071	-41530
chr2	64097961	64098068	E071	-32163
chr2	64098298	64098481	E071	-31750
chr2	64098531	64098599	E071	-31632
chr2	64098897	64098988	E071	-31243
chr2	64099188	64099330	E071	-30901
chr2	64101547	64101822	E071	-28409
chr2	64101951	64102964	E071	-27267
chr2	64103000	64103369	E071	-26862
chr2	64103606	64103732	E071	-26499
chr2	64108399	64108563	E071	-21668
chr2	64115713	64115763	E071	-14468
chr2	64115933	64116246	E071	-13985
chr2	64118923	64119039	E071	-11192
chr2	64080516	64080702	E072	-49529
chr2	64080727	64080887	E072	-49344
chr2	64080896	64080975	E072	-49256
chr2	64081019	64081300	E072	-48931
chr2	64081399	64081580	E072	-48651
chr2	64081622	64081718	E072	-48513
chr2	64081786	64081902	E072	-48329
chr2	64081918	64081983	E072	-48248
chr2	64082014	64082140	E072	-48091
chr2	64082197	64082237	E072	-47994
chr2	64082442	64082520	E072	-47711
chr2	64082567	64082640	E072	-47591
chr2	64082713	64082901	E072	-47330
chr2	64082922	64082973	E072	-47258
chr2	64096942	64097025	E072	-33206
chr2	64097129	64097179	E072	-33052
chr2	64097961	64098068	E072	-32163
chr2	64101211	64101303	E072	-28928
chr2	64101547	64101822	E072	-28409
chr2	64101951	64102964	E072	-27267
chr2	64103000	64103369	E072	-26862
chr2	64115388	64115469	E072	-14762
chr2	64115713	64115763	E072	-14468
chr2	64118923	64119039	E072	-11192
chr2	64088337	64088701	E073	-41530
chr2	64099979	64100163	E073	-30068
chr2	64101211	64101303	E073	-28928
chr2	64101547	64101822	E073	-28409
chr2	64101951	64102964	E073	-27267
chr2	64103000	64103369	E073	-26862
chr2	64115933	64116246	E073	-13985
chr2	64080516	64080702	E074	-49529
chr2	64080727	64080887	E074	-49344
chr2	64080896	64080975	E074	-49256
chr2	64081019	64081300	E074	-48931
chr2	64081399	64081580	E074	-48651
chr2	64081622	64081718	E074	-48513
chr2	64081786	64081902	E074	-48329
chr2	64081918	64081983	E074	-48248
chr2	64082014	64082140	E074	-48091
chr2	64082197	64082237	E074	-47994
chr2	64082442	64082520	E074	-47711
chr2	64082567	64082640	E074	-47591
chr2	64082713	64082901	E074	-47330
chr2	64082922	64082973	E074	-47258
chr2	64096942	64097025	E074	-33206
chr2	64097129	64097179	E074	-33052
chr2	64099979	64100163	E074	-30068
chr2	64101547	64101822	E074	-28409
chr2	64101951	64102964	E074	-27267
chr2	64103000	64103369	E074	-26862
chr2	64103606	64103732	E074	-26499
chr2	64103778	64104022	E074	-26209
chr2	64115713	64115763	E074	-14468
chr2	64118923	64119039	E074	-11192
chr2	64101547	64101822	E081	-28409
chr2	64101951	64102964	E081	-27267
chr2	64103000	64103369	E081	-26862
chr2	64103606	64103732	E081	-26499
chr2	64103778	64104022	E081	-26209
chr2	64101547	64101822	E082	-28409
chr2	64101951	64102964	E082	-27267
chr2	64103000	64103369	E082	-26862