rs3746319

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ZNF224 : Missense Variant
LOC100379224 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0284 (34542/121358,ExAC)
A==0292 (8766/29926,GnomAD)
A==0342 (9985/29118,TOPMED)
G=0286 (3722/13006,GO-ESP)
A==0399 (1997/5008,1000G)
A==0159 (612/3854,ALSPAC)
A==0162 (600/3708,TWINSUK)

Position: chr19:44108078 (GRCh38.p7) (19q13.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 7 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 70 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.44108078A>G
GRCh37.p13 chr 19	NC_000019.9:g.44612231A>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF224 transcript	NM_013398.3:c.191...NM_013398.3:c.1918A>G	K [AAA]> E [GAA]	Coding Sequence Variant
zinc finger protein 224	NP_037530.2:p.Lys...NP_037530.2:p.Lys640Glu	K [Lys]> E [Glu]	Missense Variant
ZNF224 transcript	NM_001321645.1:c....NM_001321645.1:c.1918A>G	K [AAA]> E [GAA]	Coding Sequence Variant
zinc finger protein 224	NP_001308574.1:p....NP_001308574.1:p.Lys640Glu	K [Lys]> E [Glu]	Missense Variant
ZNF224 transcript variant X1	XM_017027261.1:c....XM_017027261.1:c.1918A>G	K [AAA]> E [GAA]	Coding Sequence Variant
zinc finger protein 224 isoform X1	XP_016882750.1:p....XP_016882750.1:p.Lys640Glu	K [Lys]> E [Glu]	Missense Variant

Gene: LOC100379224, uncharacterized LOC100379224(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100379224 transcript	NR_033341.1:n.622T>C	T>C	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.533	G=0.467
1000Genomes	American	Sub	694	A=0.470	G=0.530
1000Genomes	East Asian	Sub	1008	A=0.464	G=0.536
1000Genomes	Europe	Sub	1006	A=0.191	G=0.809
1000Genomes	Global	Study-wide	5008	A=0.399	G=0.601
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=0.159	G=0.841
The Exome Aggregation Consortium	American	Sub	21970	A=0.511	G=0.488
The Exome Aggregation Consortium	Asian	Sub	25142	A=0.366	G=0.633
The Exome Aggregation Consortium	Europe	Sub	73338	A=0.189	G=0.810
The Exome Aggregation Consortium	Global	Study-wide	121358	A=0.284	G=0.715
The Exome Aggregation Consortium	Other	Sub	908	A=0.240	G=0.760
The Genome Aggregation Database	African	Sub	8694	A=0.476	G=0.524
The Genome Aggregation Database	American	Sub	838	A=0.490	G=0.510
The Genome Aggregation Database	East Asian	Sub	1612	A=0.440	G=0.560
The Genome Aggregation Database	Europe	Sub	18480	A=0.186	G=0.813
The Genome Aggregation Database	Global	Study-wide	29926	A=0.292	G=0.707
The Genome Aggregation Database	Other	Sub	302	A=0.220	G=0.780
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.342	G=0.657
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.162	G=0.838

PMID	Title	Author	Journal
27103528	Association of genetic risk factors with cognitive decline: the PATH through life project.	Andrews SJ	Neurobiol Aging
21537399	Using Fisher's method with PLINK 'LD clumped' output to compare SNP effects across Genome-wide Association Study (GWAS) datasets.	Shi H	Int J Mol Epidemiol Genet
21152065	A putative Alzheimer's disease risk allele in PCK1 influences brain atrophy in multiple sclerosis.	Xia Z	PLoS One
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet
21480501	Replication study of genome-wide associated SNPs with late-onset Alzheimer's disease.	Burns LC	Am J Med Genet B Neuropsychiatr Genet
19118814	Genome-wide association study implicates a chromosome 12 risk locus for late-onset Alzheimer disease.	Beecham GW	Am J Hum Genet
20574532	Intermediate phenotypes identify divergent pathways to Alzheimer's disease.	Shulman JM	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs3746319	0.000124	alcohol consumption	23743675

eQTL of rs3746319 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:44612231	ZNF284	ENSG00000186026.6	A>G	8.0274e-4	35934	Cerebellar_Hemisphere

meQTL of rs3746319 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 )
chr19	44618883	44619034	E068	6652
chr19	44600148	44600194	E069	-12037
chr19	44600148	44600194	E070	-12037
chr19	44618883	44619034	E070	6652
chr19	44619037	44619091	E070	6806
chr19	44619125	44619165	E070	6894
chr19	44618883	44619034	E071	6652
chr19	44600816	44600930	E082	-11301

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	44575419	44575610	E067	-36621
chr19	44575642	44577153	E067	-35078
chr19	44598047	44599722	E067	-12509
chr19	44615925	44616789	E067	3694
chr19	44616806	44618482	E067	4575
chr19	44644881	44646741	E067	32650
chr19	44575419	44575610	E068	-36621
chr19	44575642	44577153	E068	-35078
chr19	44597812	44597885	E068	-14346
chr19	44597935	44597989	E068	-14242
chr19	44598047	44599722	E068	-12509
chr19	44615787	44615827	E068	3556
chr19	44615925	44616789	E068	3694
chr19	44616806	44618482	E068	4575
chr19	44644743	44644803	E068	32512
chr19	44644881	44646741	E068	32650
chr19	44575419	44575610	E069	-36621
chr19	44575642	44577153	E069	-35078
chr19	44598047	44599722	E069	-12509
chr19	44615787	44615827	E069	3556
chr19	44615925	44616789	E069	3694
chr19	44616806	44618482	E069	4575
chr19	44644881	44646741	E069	32650
chr19	44575419	44575610	E070	-36621
chr19	44575642	44577153	E070	-35078
chr19	44598047	44599722	E070	-12509
chr19	44615925	44616789	E070	3694
chr19	44616806	44618482	E070	4575
chr19	44644743	44644803	E070	32512
chr19	44644881	44646741	E070	32650
chr19	44575419	44575610	E071	-36621
chr19	44575642	44577153	E071	-35078
chr19	44598047	44599722	E071	-12509
chr19	44615787	44615827	E071	3556
chr19	44615925	44616789	E071	3694
chr19	44616806	44618482	E071	4575
chr19	44644743	44644803	E071	32512
chr19	44644881	44646741	E071	32650
chr19	44575419	44575610	E072	-36621
chr19	44575642	44577153	E072	-35078
chr19	44598047	44599722	E072	-12509
chr19	44615925	44616789	E072	3694
chr19	44616806	44618482	E072	4575
chr19	44644743	44644803	E072	32512
chr19	44644881	44646741	E072	32650
chr19	44575419	44575610	E073	-36621
chr19	44575642	44577153	E073	-35078
chr19	44598047	44599722	E073	-12509
chr19	44615925	44616789	E073	3694
chr19	44616806	44618482	E073	4575
chr19	44644881	44646741	E073	32650
chr19	44575419	44575610	E074	-36621
chr19	44575642	44577153	E074	-35078
chr19	44598047	44599722	E074	-12509
chr19	44615925	44616789	E074	3694
chr19	44616806	44618482	E074	4575
chr19	44644881	44646741	E074	32650
chr19	44575419	44575610	E081	-36621
chr19	44575642	44577153	E081	-35078
chr19	44598047	44599722	E081	-12509
chr19	44615925	44616789	E081	3694
chr19	44616806	44618482	E081	4575
chr19	44644881	44646741	E081	32650
chr19	44575419	44575610	E082	-36621
chr19	44575642	44577153	E082	-35078
chr19	44598047	44599722	E082	-12509
chr19	44615925	44616789	E082	3694
chr19	44616806	44618482	E082	4575
chr19	44644743	44644803	E082	32512
chr19	44644881	44646741	E082	32650