rs4508518

Organism: Homo sapiens

Alleles: A>G / A>T

Gene : Feature

ZNF224 : Missense Variant
LOC100379224 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0254 (7617/29952,GnomAD)
A==0274 (7988/29118,TOPMED)
G=0235 (3065/13006,GO-ESP)
A==0356 (1782/5008,1000G)
A==0156 (603/3854,ALSPAC)
A==0161 (596/3708,TWINSUK)

Position: chr19:44107267 (GRCh38.p7) (19q13.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 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 19	NC_000019.10:g.44107267A>G
GRCh38.p7 chr 19	NC_000019.10:g.44107267A>T
GRCh37.p13 chr 19	NC_000019.9:g.44611420A>G
GRCh37.p13 chr 19	NC_000019.9:g.44611420A>T

Gene: ZNF224, zinc finger protein 224(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF224 transcript	NM_013398.3:c.110...NM_013398.3:c.1107A>G	E [GAA]> E [GAG]	Coding Sequence Variant
zinc finger protein 224	NP_037530.2:p.Glu...NP_037530.2:p.Glu369=	E [Glu]> E [Glu]	Synonymous Variant
ZNF224 transcript	NM_013398.3:c.110...NM_013398.3:c.1107A>T	E [GAA]> D [GAT]	Coding Sequence Variant
zinc finger protein 224	NP_037530.2:p.Glu...NP_037530.2:p.Glu369Asp	E [Glu]> D [Asp]	Missense Variant
ZNF224 transcript	NM_001321645.1:c....NM_001321645.1:c.1107A>G	E [GAA]> E [GAG]	Coding Sequence Variant
zinc finger protein 224	NP_001308574.1:p....NP_001308574.1:p.Glu369=	E [Glu]> E [Glu]	Synonymous Variant
ZNF224 transcript	NM_001321645.1:c....NM_001321645.1:c.1107A>T	E [GAA]> D [GAT]	Coding Sequence Variant
zinc finger protein 224	NP_001308574.1:p....NP_001308574.1:p.Glu369Asp	E [Glu]> D [Asp]	Missense Variant
ZNF224 transcript variant X1	XM_017027261.1:c....XM_017027261.1:c.1107A>G	E [GAA]> E [GAG]	Coding Sequence Variant
zinc finger protein 224 isoform X1	XP_016882750.1:p....XP_016882750.1:p.Glu369=	E [Glu]> E [Glu]	Synonymous Variant
ZNF224 transcript variant X1	XM_017027261.1:c....XM_017027261.1:c.1107A>T	E [GAA]> D [GAT]	Coding Sequence Variant
zinc finger protein 224 isoform X1	XP_016882750.1:p....XP_016882750.1:p.Glu369Asp	E [Glu]> D [Asp]	Missense Variant

Gene: LOC100379224, uncharacterized LOC100379224(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100379224 transcript	NR_033341.1:n.143...NR_033341.1:n.1433T>C	T>C	Non Coding Transcript Variant
LOC100379224 transcript	NR_033341.1:n.143...NR_033341.1:n.1433T>A	T>A	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.380	G=0.620
1000Genomes	American	Sub	694	A=0.450	G=0.550
1000Genomes	East Asian	Sub	1008	A=0.469	G=0.531
1000Genomes	Europe	Sub	1006	A=0.191	G=0.809
1000Genomes	Global	Study-wide	5008	A=0.356	G=0.644
1000Genomes	South Asian	Sub	978	A=0.310	G=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.156	G=0.844
The Genome Aggregation Database	African	Sub	8718	A=0.327	G=0.673
The Genome Aggregation Database	American	Sub	838	A=0.480	G=0.520
The Genome Aggregation Database	East Asian	Sub	1608	A=0.444	G=0.556
The Genome Aggregation Database	Europe	Sub	18486	A=0.194	G=0.805
The Genome Aggregation Database	Global	Study-wide	29952	A=0.254	G=0.745
The Genome Aggregation Database	Other	Sub	302	A=0.200	G=0.800
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.274	G=0.725
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.161	G=0.839

PMID	Title	Author	Journal
19118814	Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease.	Beecham GW	Am J Hum Genet
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
rs4508518	0.000145	alcohol consumption	23743675

eQTL of rs4508518 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:44611420	ZNF284	ENSG00000186026.6	A>G	8.0274e-4	35123	Cerebellar_Hemisphere

meQTL of rs4508518 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.