rs6070956

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

PHACTR3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0481 (14404/29918,GnomAD)
T=0466 (13584/29118,TOPMED)
T=0498 (2495/5008,1000G)
C==0376 (1449/3854,ALSPAC)
C==0375 (1392/3708,TWINSUK)

Position: chr20:59809755 (GRCh38.p7) (20q13.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.59809755C>G
GRCh38.p7 chr 20	NC_000020.11:g.59809755C>T
GRCh37.p13 chr 20	NC_000020.10:g.58384810C>G
GRCh37.p13 chr 20	NC_000020.10:g.58384810C>T
PHACTR3 RefSeqGene	NG_029537.1:g.237247C>G
PHACTR3 RefSeqGene	NG_029537.1:g.237247C>T

Gene: PHACTR3, phosphatase and actin regulator 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PHACTR3 transcript variant 4	NM_001199505.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 5	NM_001199506.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 6	NM_001281507.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 1	NM_080672.4:c.	N/A	Intron Variant
PHACTR3 transcript variant 2	NM_183244.1:c.	N/A	Intron Variant
PHACTR3 transcript variant 3	NM_183246.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X2	XM_011528525.2:c.	N/A	Intron Variant
PHACTR3 transcript variant X4	XM_011528526.2:c.	N/A	Intron Variant
PHACTR3 transcript variant X1	XM_017027626.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X3	XM_017027627.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X5	XM_017027628.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X6	XM_017027629.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X7	XM_017027630.1:c.	N/A	Intron Variant
PHACTR3 transcript variant X8	XM_017027631.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.749	T=0.251
1000Genomes	American	Sub	694	C=0.330	T=0.670
1000Genomes	East Asian	Sub	1008	C=0.442	T=0.558
1000Genomes	Europe	Sub	1006	C=0.411	T=0.589
1000Genomes	Global	Study-wide	5008	C=0.502	T=0.498
1000Genomes	South Asian	Sub	978	C=0.440	T=0.560
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.376	T=0.624
The Genome Aggregation Database	African	Sub	8706	C=0.711	T=0.289
The Genome Aggregation Database	American	Sub	836	C=0.340	T=0.660
The Genome Aggregation Database	East Asian	Sub	1608	C=0.464	T=0.536
The Genome Aggregation Database	Europe	Sub	18466	C=0.380	T=0.619
The Genome Aggregation Database	Global	Study-wide	29918	C=0.481	T=0.518
The Genome Aggregation Database	Other	Sub	302	C=0.550	T=0.450
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.533	T=0.466
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.375	T=0.625

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs6070956	1.58E-05	alcohol consumption	23743675

eQTL of rs6070956 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 rs6070956 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.