rs2029211

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

ZGRF1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0403 (11929/29598,GnomAD)
T==0383 (11175/29118,TOPMED)
T==0275 (1375/5008,1000G)
T==0421 (1624/3854,ALSPAC)
T==0408 (1513/3708,TWINSUK)

Position: chr4:112566978 (GRCh38.p7) (4q25)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 5 Enhancers around

Promoter: 4 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.112566978T>C
GRCh37.p13 chr 4	NC_000004.11:g.113488134T>C

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 X11	XM_011532096.2: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 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	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.386	C=0.614
1000Genomes	American	Sub	694	T=0.260	C=0.740
1000Genomes	East Asian	Sub	1008	T=0.059	C=0.941
1000Genomes	Europe	Sub	1006	T=0.427	C=0.573
1000Genomes	Global	Study-wide	5008	T=0.275	C=0.725
1000Genomes	South Asian	Sub	978	T=0.200	C=0.800
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.421	C=0.579
The Genome Aggregation Database	African	Sub	8654	T=0.387	C=0.613
The Genome Aggregation Database	American	Sub	830	T=0.250	C=0.750
The Genome Aggregation Database	East Asian	Sub	1620	T=0.049	C=0.951
The Genome Aggregation Database	Europe	Sub	18192	T=0.448	C=0.551
The Genome Aggregation Database	Global	Study-wide	29598	T=0.403	C=0.597
The Genome Aggregation Database	Other	Sub	302	T=0.470	C=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.383	C=0.616
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.408	C=0.592

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
rs2029211	0.00087	alcohol dependence	20201924

eQTL of rs2029211 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 rs2029211 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	113440778	113440858	E081	-47276
chr4	113442934	113443192	E081	-44942
chr4	113443369	113443617	E081	-44517
chr4	113443634	113443737	E081	-44397
chr4	113442934	113443192	E082	-44942

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr4	113444033	113445706	E068	-42428
chr4	113444033	113445706	E069	-42428
chr4	113444033	113445706	E072	-42428
chr4	113444033	113445706	E082	-42428