rs10420143

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ZNF224 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0205 (6153/29934,GnomAD)
A==0229 (6695/29118,TOPMED)
A==0308 (1543/5008,1000G)
A==0122 (469/3854,ALSPAC)
A==0121 (448/3708,TWINSUK)

Position: chr19:44103929 (GRCh38.p7) (19q13.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 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.44103929A>G
GRCh37.p13 chr 19	NC_000019.9:g.44608082A>G

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	A=0.312	G=0.688
1000Genomes	American	Sub	694	A=0.430	G=0.570
1000Genomes	East Asian	Sub	1008	A=0.475	G=0.525
1000Genomes	Europe	Sub	1006	A=0.142	G=0.858
1000Genomes	Global	Study-wide	5008	A=0.308	G=0.692
1000Genomes	South Asian	Sub	978	A=0.220	G=0.780
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.122	G=0.878
The Genome Aggregation Database	African	Sub	8702	A=0.266	G=0.734
The Genome Aggregation Database	American	Sub	838	A=0.450	G=0.550
The Genome Aggregation Database	East Asian	Sub	1610	A=0.455	G=0.545
The Genome Aggregation Database	Europe	Sub	18482	A=0.145	G=0.855
The Genome Aggregation Database	Global	Study-wide	29934	A=0.205	G=0.794
The Genome Aggregation Database	Other	Sub	302	A=0.170	G=0.830
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.229	G=0.770
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.121	G=0.879

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
rs10420143	2.75E-05	alcohol consumption	23743675

eQTL of rs10420143 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 rs10420143 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	10801
chr19	44600148	44600194	E069	-7888
chr19	44600148	44600194	E070	-7888
chr19	44618883	44619034	E070	10801
chr19	44619037	44619091	E070	10955
chr19	44619125	44619165	E070	11043
chr19	44618883	44619034	E071	10801
chr19	44600816	44600930	E082	-7152

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	44575419	44575610	E067	-32472
chr19	44575642	44577153	E067	-30929
chr19	44598047	44599722	E067	-8360
chr19	44615925	44616789	E067	7843
chr19	44616806	44618482	E067	8724
chr19	44644881	44646741	E067	36799
chr19	44575419	44575610	E068	-32472
chr19	44575642	44577153	E068	-30929
chr19	44597812	44597885	E068	-10197
chr19	44597935	44597989	E068	-10093
chr19	44598047	44599722	E068	-8360
chr19	44615787	44615827	E068	7705
chr19	44615925	44616789	E068	7843
chr19	44616806	44618482	E068	8724
chr19	44644743	44644803	E068	36661
chr19	44644881	44646741	E068	36799
chr19	44575419	44575610	E069	-32472
chr19	44575642	44577153	E069	-30929
chr19	44598047	44599722	E069	-8360
chr19	44615787	44615827	E069	7705
chr19	44615925	44616789	E069	7843
chr19	44616806	44618482	E069	8724
chr19	44644881	44646741	E069	36799
chr19	44575419	44575610	E070	-32472
chr19	44575642	44577153	E070	-30929
chr19	44598047	44599722	E070	-8360
chr19	44615925	44616789	E070	7843
chr19	44616806	44618482	E070	8724
chr19	44644743	44644803	E070	36661
chr19	44644881	44646741	E070	36799
chr19	44575419	44575610	E071	-32472
chr19	44575642	44577153	E071	-30929
chr19	44598047	44599722	E071	-8360
chr19	44615787	44615827	E071	7705
chr19	44615925	44616789	E071	7843
chr19	44616806	44618482	E071	8724
chr19	44644743	44644803	E071	36661
chr19	44644881	44646741	E071	36799
chr19	44575419	44575610	E072	-32472
chr19	44575642	44577153	E072	-30929
chr19	44598047	44599722	E072	-8360
chr19	44615925	44616789	E072	7843
chr19	44616806	44618482	E072	8724
chr19	44644743	44644803	E072	36661
chr19	44644881	44646741	E072	36799
chr19	44575419	44575610	E073	-32472
chr19	44575642	44577153	E073	-30929
chr19	44598047	44599722	E073	-8360
chr19	44615925	44616789	E073	7843
chr19	44616806	44618482	E073	8724
chr19	44644881	44646741	E073	36799
chr19	44575419	44575610	E074	-32472
chr19	44575642	44577153	E074	-30929
chr19	44598047	44599722	E074	-8360
chr19	44615925	44616789	E074	7843
chr19	44616806	44618482	E074	8724
chr19	44644881	44646741	E074	36799
chr19	44575419	44575610	E081	-32472
chr19	44575642	44577153	E081	-30929
chr19	44598047	44599722	E081	-8360
chr19	44615925	44616789	E081	7843
chr19	44616806	44618482	E081	8724
chr19	44644881	44646741	E081	36799
chr19	44575419	44575610	E082	-32472
chr19	44575642	44577153	E082	-30929
chr19	44598047	44599722	E082	-8360
chr19	44615925	44616789	E082	7843
chr19	44616806	44618482	E082	8724
chr19	44644743	44644803	E082	36661
chr19	44644881	44646741	E082	36799