rs7249827

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

ZNF224 : Intron Variant
LOC100379224 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0149 (4467/29966,GnomAD)
C==0145 (4245/29118,TOPMED)
C==0203 (1019/5008,1000G)
C==0115 (443/3854,ALSPAC)
C==0117 (432/3708,TWINSUK)

Position: chr19:44105876 (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.44105876C>A
GRCh37.p13 chr 19	NC_000019.9:g.44610029C>A

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

Gene: LOC100379224, uncharacterized LOC100379224(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100379224 transcript	NR_033341.1:n.282...NR_033341.1:n.2824G>T	G>T	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.116	A=0.884
1000Genomes	American	Sub	694	C=0.250	A=0.750
1000Genomes	East Asian	Sub	1008	C=0.383	A=0.617
1000Genomes	Europe	Sub	1006	C=0.120	A=0.880
1000Genomes	Global	Study-wide	5008	C=0.203	A=0.797
1000Genomes	South Asian	Sub	978	C=0.190	A=0.810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.115	A=0.885
The Genome Aggregation Database	African	Sub	8720	C=0.132	A=0.868
The Genome Aggregation Database	American	Sub	834	C=0.250	A=0.750
The Genome Aggregation Database	East Asian	Sub	1618	C=0.390	A=0.610
The Genome Aggregation Database	Europe	Sub	18492	C=0.131	A=0.868
The Genome Aggregation Database	Global	Study-wide	29966	C=0.149	A=0.850
The Genome Aggregation Database	Other	Sub	302	C=0.170	A=0.830
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.145	A=0.854
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.117	A=0.883

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
rs7249827	0.000165	alcohol consumption	23743675

eQTL of rs7249827 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 rs7249827 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	8854
chr19	44600148	44600194	E069	-9835
chr19	44600148	44600194	E070	-9835
chr19	44618883	44619034	E070	8854
chr19	44619037	44619091	E070	9008
chr19	44619125	44619165	E070	9096
chr19	44618883	44619034	E071	8854
chr19	44600816	44600930	E082	-9099

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	44575419	44575610	E067	-34419
chr19	44575642	44577153	E067	-32876
chr19	44598047	44599722	E067	-10307
chr19	44615925	44616789	E067	5896
chr19	44616806	44618482	E067	6777
chr19	44644881	44646741	E067	34852
chr19	44575419	44575610	E068	-34419
chr19	44575642	44577153	E068	-32876
chr19	44597812	44597885	E068	-12144
chr19	44597935	44597989	E068	-12040
chr19	44598047	44599722	E068	-10307
chr19	44615787	44615827	E068	5758
chr19	44615925	44616789	E068	5896
chr19	44616806	44618482	E068	6777
chr19	44644743	44644803	E068	34714
chr19	44644881	44646741	E068	34852
chr19	44575419	44575610	E069	-34419
chr19	44575642	44577153	E069	-32876
chr19	44598047	44599722	E069	-10307
chr19	44615787	44615827	E069	5758
chr19	44615925	44616789	E069	5896
chr19	44616806	44618482	E069	6777
chr19	44644881	44646741	E069	34852
chr19	44575419	44575610	E070	-34419
chr19	44575642	44577153	E070	-32876
chr19	44598047	44599722	E070	-10307
chr19	44615925	44616789	E070	5896
chr19	44616806	44618482	E070	6777
chr19	44644743	44644803	E070	34714
chr19	44644881	44646741	E070	34852
chr19	44575419	44575610	E071	-34419
chr19	44575642	44577153	E071	-32876
chr19	44598047	44599722	E071	-10307
chr19	44615787	44615827	E071	5758
chr19	44615925	44616789	E071	5896
chr19	44616806	44618482	E071	6777
chr19	44644743	44644803	E071	34714
chr19	44644881	44646741	E071	34852
chr19	44575419	44575610	E072	-34419
chr19	44575642	44577153	E072	-32876
chr19	44598047	44599722	E072	-10307
chr19	44615925	44616789	E072	5896
chr19	44616806	44618482	E072	6777
chr19	44644743	44644803	E072	34714
chr19	44644881	44646741	E072	34852
chr19	44575419	44575610	E073	-34419
chr19	44575642	44577153	E073	-32876
chr19	44598047	44599722	E073	-10307
chr19	44615925	44616789	E073	5896
chr19	44616806	44618482	E073	6777
chr19	44644881	44646741	E073	34852
chr19	44575419	44575610	E074	-34419
chr19	44575642	44577153	E074	-32876
chr19	44598047	44599722	E074	-10307
chr19	44615925	44616789	E074	5896
chr19	44616806	44618482	E074	6777
chr19	44644881	44646741	E074	34852
chr19	44575419	44575610	E081	-34419
chr19	44575642	44577153	E081	-32876
chr19	44598047	44599722	E081	-10307
chr19	44615925	44616789	E081	5896
chr19	44616806	44618482	E081	6777
chr19	44644881	44646741	E081	34852
chr19	44575419	44575610	E082	-34419
chr19	44575642	44577153	E082	-32876
chr19	44598047	44599722	E082	-10307
chr19	44615925	44616789	E082	5896
chr19	44616806	44618482	E082	6777
chr19	44644743	44644803	E082	34714
chr19	44644881	44646741	E082	34852