rs28539456

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

ZNF224 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0251 (7527/29952,GnomAD)
G==0301 (8781/29118,TOPMED)
G==0362 (1814/5008,1000G)
G==0123 (474/3854,ALSPAC)
G==0123 (456/3708,TWINSUK)

Position: chr19:44103394 (GRCh38.p7) (19q13.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 9 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.44103394G>T
GRCh37.p13 chr 19	NC_000019.9:g.44607547G>T

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

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF224 transcript	NM_001321645.1:c.	N/A	Intron Variant
ZNF224 transcript	NM_013398.3:c.	N/A	Intron Variant
ZNF224 transcript variant X1	XM_017027261.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.498	T=0.502
1000Genomes	American	Sub	694	G=0.450	T=0.550
1000Genomes	East Asian	Sub	1008	G=0.474	T=0.526
1000Genomes	Europe	Sub	1006	G=0.143	T=0.857
1000Genomes	Global	Study-wide	5008	G=0.362	T=0.638
1000Genomes	South Asian	Sub	978	G=0.230	T=0.770
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.123	T=0.877
The Genome Aggregation Database	African	Sub	8704	G=0.420	T=0.580
The Genome Aggregation Database	American	Sub	838	G=0.460	T=0.540
The Genome Aggregation Database	East Asian	Sub	1616	G=0.454	T=0.546
The Genome Aggregation Database	Europe	Sub	18492	G=0.145	T=0.854
The Genome Aggregation Database	Global	Study-wide	29952	G=0.251	T=0.748
The Genome Aggregation Database	Other	Sub	302	G=0.190	T=0.810
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.301	T=0.698
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.123	T=0.877

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
rs28539456	8.92E-05	alcohol consumption	23743675

eQTL of rs28539456 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 rs28539456 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	11336
chr19	44600148	44600194	E069	-7353
chr19	44557933	44557994	E070	-49553
chr19	44600148	44600194	E070	-7353
chr19	44618883	44619034	E070	11336
chr19	44619037	44619091	E070	11490
chr19	44619125	44619165	E070	11578
chr19	44618883	44619034	E071	11336
chr19	44600816	44600930	E082	-6617

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	44575419	44575610	E067	-31937
chr19	44575642	44577153	E067	-30394
chr19	44598047	44599722	E067	-7825
chr19	44615925	44616789	E067	8378
chr19	44616806	44618482	E067	9259
chr19	44644881	44646741	E067	37334
chr19	44575419	44575610	E068	-31937
chr19	44575642	44577153	E068	-30394
chr19	44597812	44597885	E068	-9662
chr19	44597935	44597989	E068	-9558
chr19	44598047	44599722	E068	-7825
chr19	44615787	44615827	E068	8240
chr19	44615925	44616789	E068	8378
chr19	44616806	44618482	E068	9259
chr19	44644743	44644803	E068	37196
chr19	44644881	44646741	E068	37334
chr19	44575419	44575610	E069	-31937
chr19	44575642	44577153	E069	-30394
chr19	44598047	44599722	E069	-7825
chr19	44615787	44615827	E069	8240
chr19	44615925	44616789	E069	8378
chr19	44616806	44618482	E069	9259
chr19	44644881	44646741	E069	37334
chr19	44575419	44575610	E070	-31937
chr19	44575642	44577153	E070	-30394
chr19	44598047	44599722	E070	-7825
chr19	44615925	44616789	E070	8378
chr19	44616806	44618482	E070	9259
chr19	44644743	44644803	E070	37196
chr19	44644881	44646741	E070	37334
chr19	44575419	44575610	E071	-31937
chr19	44575642	44577153	E071	-30394
chr19	44598047	44599722	E071	-7825
chr19	44615787	44615827	E071	8240
chr19	44615925	44616789	E071	8378
chr19	44616806	44618482	E071	9259
chr19	44644743	44644803	E071	37196
chr19	44644881	44646741	E071	37334
chr19	44575419	44575610	E072	-31937
chr19	44575642	44577153	E072	-30394
chr19	44598047	44599722	E072	-7825
chr19	44615925	44616789	E072	8378
chr19	44616806	44618482	E072	9259
chr19	44644743	44644803	E072	37196
chr19	44644881	44646741	E072	37334
chr19	44575419	44575610	E073	-31937
chr19	44575642	44577153	E073	-30394
chr19	44598047	44599722	E073	-7825
chr19	44615925	44616789	E073	8378
chr19	44616806	44618482	E073	9259
chr19	44644881	44646741	E073	37334
chr19	44575419	44575610	E074	-31937
chr19	44575642	44577153	E074	-30394
chr19	44598047	44599722	E074	-7825
chr19	44615925	44616789	E074	8378
chr19	44616806	44618482	E074	9259
chr19	44644881	44646741	E074	37334
chr19	44575419	44575610	E081	-31937
chr19	44575642	44577153	E081	-30394
chr19	44598047	44599722	E081	-7825
chr19	44615925	44616789	E081	8378
chr19	44616806	44618482	E081	9259
chr19	44644881	44646741	E081	37334
chr19	44575419	44575610	E082	-31937
chr19	44575642	44577153	E082	-30394
chr19	44598047	44599722	E082	-7825
chr19	44615925	44616789	E082	8378
chr19	44616806	44618482	E082	9259
chr19	44644743	44644803	E082	37196
chr19	44644881	44646741	E082	37334