rs3172

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

ZNF224 : Intron Variant
LOC100379224 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0358 (10712/29916,GnomAD)
C==0431 (12573/29118,TOPMED)
C==0461 (2310/5008,1000G)
C==0158 (609/3854,ALSPAC)
C==0161 (597/3708,TWINSUK)

Position: chr19:44105693 (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.44105693C>G
GRCh37.p13 chr 19	NC_000019.9:g.44609846C>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

Gene: LOC100379224, uncharacterized LOC100379224(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100379224 transcript	NR_033341.1:n.300...NR_033341.1:n.3007G>C	G>C	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.763	G=0.237
1000Genomes	American	Sub	694	C=0.490	G=0.510
1000Genomes	East Asian	Sub	1008	C=0.468	G=0.532
1000Genomes	Europe	Sub	1006	C=0.193	G=0.807
1000Genomes	Global	Study-wide	5008	C=0.461	G=0.539
1000Genomes	South Asian	Sub	978	C=0.300	G=0.700
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.158	G=0.842
The Genome Aggregation Database	African	Sub	8698	C=0.677	G=0.323
The Genome Aggregation Database	American	Sub	832	C=0.500	G=0.500
The Genome Aggregation Database	East Asian	Sub	1614	C=0.447	G=0.553
The Genome Aggregation Database	Europe	Sub	18470	C=0.196	G=0.803
The Genome Aggregation Database	Global	Study-wide	29916	C=0.358	G=0.641
The Genome Aggregation Database	Other	Sub	302	C=0.230	G=0.770
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.431	G=0.568
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.161	G=0.839

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
rs3172	0.000159	alcohol consumption	23743675

eQTL of rs3172 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr19:44609846	ZNF284	ENSG00000186026.6	C>G	6.4241e-4	33549	Cerebellum
Chr19:44609846	ZNF284	ENSG00000186026.6	C>G	8.0274e-4	33549	Cerebellar_Hemisphere

meQTL of rs3172 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	9037
chr19	44600148	44600194	E069	-9652
chr19	44600148	44600194	E070	-9652
chr19	44618883	44619034	E070	9037
chr19	44619037	44619091	E070	9191
chr19	44619125	44619165	E070	9279
chr19	44618883	44619034	E071	9037
chr19	44600816	44600930	E082	-8916

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	44575419	44575610	E067	-34236
chr19	44575642	44577153	E067	-32693
chr19	44598047	44599722	E067	-10124
chr19	44615925	44616789	E067	6079
chr19	44616806	44618482	E067	6960
chr19	44644881	44646741	E067	35035
chr19	44575419	44575610	E068	-34236
chr19	44575642	44577153	E068	-32693
chr19	44597812	44597885	E068	-11961
chr19	44597935	44597989	E068	-11857
chr19	44598047	44599722	E068	-10124
chr19	44615787	44615827	E068	5941
chr19	44615925	44616789	E068	6079
chr19	44616806	44618482	E068	6960
chr19	44644743	44644803	E068	34897
chr19	44644881	44646741	E068	35035
chr19	44575419	44575610	E069	-34236
chr19	44575642	44577153	E069	-32693
chr19	44598047	44599722	E069	-10124
chr19	44615787	44615827	E069	5941
chr19	44615925	44616789	E069	6079
chr19	44616806	44618482	E069	6960
chr19	44644881	44646741	E069	35035
chr19	44575419	44575610	E070	-34236
chr19	44575642	44577153	E070	-32693
chr19	44598047	44599722	E070	-10124
chr19	44615925	44616789	E070	6079
chr19	44616806	44618482	E070	6960
chr19	44644743	44644803	E070	34897
chr19	44644881	44646741	E070	35035
chr19	44575419	44575610	E071	-34236
chr19	44575642	44577153	E071	-32693
chr19	44598047	44599722	E071	-10124
chr19	44615787	44615827	E071	5941
chr19	44615925	44616789	E071	6079
chr19	44616806	44618482	E071	6960
chr19	44644743	44644803	E071	34897
chr19	44644881	44646741	E071	35035
chr19	44575419	44575610	E072	-34236
chr19	44575642	44577153	E072	-32693
chr19	44598047	44599722	E072	-10124
chr19	44615925	44616789	E072	6079
chr19	44616806	44618482	E072	6960
chr19	44644743	44644803	E072	34897
chr19	44644881	44646741	E072	35035
chr19	44575419	44575610	E073	-34236
chr19	44575642	44577153	E073	-32693
chr19	44598047	44599722	E073	-10124
chr19	44615925	44616789	E073	6079
chr19	44616806	44618482	E073	6960
chr19	44644881	44646741	E073	35035
chr19	44575419	44575610	E074	-34236
chr19	44575642	44577153	E074	-32693
chr19	44598047	44599722	E074	-10124
chr19	44615925	44616789	E074	6079
chr19	44616806	44618482	E074	6960
chr19	44644881	44646741	E074	35035
chr19	44575419	44575610	E081	-34236
chr19	44575642	44577153	E081	-32693
chr19	44598047	44599722	E081	-10124
chr19	44615925	44616789	E081	6079
chr19	44616806	44618482	E081	6960
chr19	44644881	44646741	E081	35035
chr19	44575419	44575610	E082	-34236
chr19	44575642	44577153	E082	-32693
chr19	44598047	44599722	E082	-10124
chr19	44615925	44616789	E082	6079
chr19	44616806	44618482	E082	6960
chr19	44644743	44644803	E082	34897
chr19	44644881	44646741	E082	35035