rs1486865

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ZGRF1 : Intron Variant
LOC105377372 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0411 (12282/29880,GnomAD)
A==0395 (11520/29118,TOPMED)
A==0277 (1388/5008,1000G)
A==0435 (1675/3854,ALSPAC)
A==0418 (1551/3708,TWINSUK)

Position: chr4:112544495 (GRCh38.p7) (4q25)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 12 Enhancers around

Promoter: 15 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.112544495A>G
GRCh37.p13 chr 4	NC_000004.11:g.113465651A>G

Gene: ZGRF1, zinc finger GRF-type containing 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZGRF1 transcript variant 1	NM_018392.4:c.	N/A	Intron Variant
ZGRF1 transcript variant X1	XM_005263115.3:c.	N/A	Intron Variant
ZGRF1 transcript variant X2	XM_011532091.2:c.	N/A	Intron Variant
ZGRF1 transcript variant X3	XM_011532092.2:c.	N/A	Intron Variant
ZGRF1 transcript variant X5	XM_011532093.2:c.	N/A	Intron Variant
ZGRF1 transcript variant X6	XM_011532094.2:c.	N/A	Intron Variant
ZGRF1 transcript variant X12	XM_011532097.2:c.	N/A	Intron Variant
ZGRF1 transcript variant X13	XM_011532098.2:c.	N/A	Intron Variant
ZGRF1 transcript variant X14	XM_011532099.2:c.	N/A	Intron Variant
ZGRF1 transcript variant X4	XM_017008369.1:c.	N/A	Intron Variant
ZGRF1 transcript variant X5	XM_017008370.1:c.	N/A	Intron Variant
ZGRF1 transcript variant X7	XM_017008371.1:c.	N/A	Intron Variant
ZGRF1 transcript variant X15	XM_017008372.1:c.	N/A	Intron Variant
ZGRF1 transcript variant X16	XM_017008373.1:c.	N/A	Intron Variant
ZGRF1 transcript variant X11	XM_011532096.2:c.	N/A	Genic Downstream Transcript Variant
ZGRF1 transcript variant X10	XR_001741282.1:n.	N/A	Intron Variant
ZGRF1 transcript variant X8	XR_938763.1:n.	N/A	Intron Variant
ZGRF1 transcript variant X9	XR_938764.1:n.	N/A	Genic Downstream Transcript Variant

Gene: LOC105377372, uncharacterized LOC105377372(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105377372 transcript	XR_001741416.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.387	G=0.613
1000Genomes	American	Sub	694	A=0.260	G=0.740
1000Genomes	East Asian	Sub	1008	A=0.059	G=0.941
1000Genomes	Europe	Sub	1006	A=0.436	G=0.564
1000Genomes	Global	Study-wide	5008	A=0.277	G=0.723
1000Genomes	South Asian	Sub	978	A=0.200	G=0.800
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.435	G=0.565
The Genome Aggregation Database	African	Sub	8684	A=0.390	G=0.610
The Genome Aggregation Database	American	Sub	838	A=0.260	G=0.740
The Genome Aggregation Database	East Asian	Sub	1614	A=0.050	G=0.950
The Genome Aggregation Database	Europe	Sub	18442	A=0.458	G=0.541
The Genome Aggregation Database	Global	Study-wide	29880	A=0.411	G=0.589
The Genome Aggregation Database	Other	Sub	302	A=0.470	G=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.395	G=0.604
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.418	G=0.582

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
rs1486865	0.000618	alcohol dependence	20201924

eQTL of rs1486865 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr4:113465651	LARP7	ENSG00000174720.11	A>G	2.1704e-3	-92495	Cerebellar_Hemisphere

meQTL of rs1486865 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 )
chr4	113429664	113429829	E068	-35822
chr4	113429943	113429998	E068	-35653
chr4	113430174	113430332	E068	-35319
chr4	113430174	113430332	E069	-35319
chr4	113429664	113429829	E081	-35822
chr4	113429943	113429998	E081	-35653
chr4	113430174	113430332	E081	-35319
chr4	113440778	113440858	E081	-24793
chr4	113442934	113443192	E081	-22459
chr4	113443369	113443617	E081	-22034
chr4	113443634	113443737	E081	-21914
chr4	113442934	113443192	E082	-22459

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr4	113436393	113438917	E067	-26734
chr4	113436393	113438917	E068	-26734
chr4	113444033	113445706	E068	-19945
chr4	113436393	113438917	E069	-26734
chr4	113444033	113445706	E069	-19945
chr4	113436393	113438917	E071	-26734
chr4	113444033	113445706	E072	-19945
chr4	113434947	113436380	E073	-29271
chr4	113436393	113438917	E073	-26734
chr4	113436393	113438917	E074	-26734
chr4	113434947	113436380	E081	-29271
chr4	113434490	113434650	E082	-31001
chr4	113434947	113436380	E082	-29271
chr4	113436393	113438917	E082	-26734
chr4	113444033	113445706	E082	-19945