rs2284978

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ZNF225 : Intron Variant
LOC100379224 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0134 (4023/29968,GnomAD)
A==0124 (3610/29118,TOPMED)
A==0189 (946/5008,1000G)
A==0114 (440/3854,ALSPAC)
A==0115 (428/3708,TWINSUK)

Position: chr19:44113157 (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.44113157A>G
GRCh37.p13 chr 19	NC_000019.9:g.44617310A>G

Gene: ZNF225, zinc finger protein 225(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF225 transcript variant 2	NM_001321685.1:c.	N/A	Genic Upstream Transcript Variant
ZNF225 transcript variant 1	NM_013362.3:c.	N/A	Genic Upstream Transcript Variant
ZNF225 transcript variant X2	XM_011527286.2:c.	N/A	Intron Variant
ZNF225 transcript variant X3	XM_005259223.3:c.	N/A	Genic Upstream Transcript Variant
ZNF225 transcript variant X1	XM_011527285.2:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC100379224, uncharacterized LOC100379224(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100379224 transcript	NR_033341.1:n.27T>C	T>C	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.065	G=0.935
1000Genomes	American	Sub	694	A=0.240	G=0.760
1000Genomes	East Asian	Sub	1008	A=0.380	G=0.620
1000Genomes	Europe	Sub	1006	A=0.119	G=0.881
1000Genomes	Global	Study-wide	5008	A=0.189	G=0.811
1000Genomes	South Asian	Sub	978	A=0.190	G=0.810
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.114	G=0.886
The Genome Aggregation Database	African	Sub	8722	A=0.082	G=0.918
The Genome Aggregation Database	American	Sub	836	A=0.250	G=0.750
The Genome Aggregation Database	East Asian	Sub	1610	A=0.385	G=0.615
The Genome Aggregation Database	Europe	Sub	18498	A=0.131	G=0.868
The Genome Aggregation Database	Global	Study-wide	29968	A=0.134	G=0.865
The Genome Aggregation Database	Other	Sub	302	A=0.170	G=0.830
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.124	G=0.876
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.115	G=0.885

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
rs2284978	0.000118	alcohol consumption	23743675

eQTL of rs2284978 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 rs2284978 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	1573
chr19	44600148	44600194	E069	-17116
chr19	44600148	44600194	E070	-17116
chr19	44618883	44619034	E070	1573
chr19	44619037	44619091	E070	1727
chr19	44619125	44619165	E070	1815
chr19	44618883	44619034	E071	1573
chr19	44600816	44600930	E082	-16380

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	44575419	44575610	E067	-41700
chr19	44575642	44577153	E067	-40157
chr19	44598047	44599722	E067	-17588
chr19	44615925	44616789	E067	-521
chr19	44616806	44618482	E067	0
chr19	44644881	44646741	E067	27571
chr19	44575419	44575610	E068	-41700
chr19	44575642	44577153	E068	-40157
chr19	44597812	44597885	E068	-19425
chr19	44597935	44597989	E068	-19321
chr19	44598047	44599722	E068	-17588
chr19	44615787	44615827	E068	-1483
chr19	44615925	44616789	E068	-521
chr19	44616806	44618482	E068	0
chr19	44644743	44644803	E068	27433
chr19	44644881	44646741	E068	27571
chr19	44575419	44575610	E069	-41700
chr19	44575642	44577153	E069	-40157
chr19	44598047	44599722	E069	-17588
chr19	44615787	44615827	E069	-1483
chr19	44615925	44616789	E069	-521
chr19	44616806	44618482	E069	0
chr19	44644881	44646741	E069	27571
chr19	44575419	44575610	E070	-41700
chr19	44575642	44577153	E070	-40157
chr19	44598047	44599722	E070	-17588
chr19	44615925	44616789	E070	-521
chr19	44616806	44618482	E070	0
chr19	44644743	44644803	E070	27433
chr19	44644881	44646741	E070	27571
chr19	44575419	44575610	E071	-41700
chr19	44575642	44577153	E071	-40157
chr19	44598047	44599722	E071	-17588
chr19	44615787	44615827	E071	-1483
chr19	44615925	44616789	E071	-521
chr19	44616806	44618482	E071	0
chr19	44644743	44644803	E071	27433
chr19	44644881	44646741	E071	27571
chr19	44575419	44575610	E072	-41700
chr19	44575642	44577153	E072	-40157
chr19	44598047	44599722	E072	-17588
chr19	44615925	44616789	E072	-521
chr19	44616806	44618482	E072	0
chr19	44644743	44644803	E072	27433
chr19	44644881	44646741	E072	27571
chr19	44575419	44575610	E073	-41700
chr19	44575642	44577153	E073	-40157
chr19	44598047	44599722	E073	-17588
chr19	44615925	44616789	E073	-521
chr19	44616806	44618482	E073	0
chr19	44644881	44646741	E073	27571
chr19	44575419	44575610	E074	-41700
chr19	44575642	44577153	E074	-40157
chr19	44598047	44599722	E074	-17588
chr19	44615925	44616789	E074	-521
chr19	44616806	44618482	E074	0
chr19	44644881	44646741	E074	27571
chr19	44575419	44575610	E081	-41700
chr19	44575642	44577153	E081	-40157
chr19	44598047	44599722	E081	-17588
chr19	44615925	44616789	E081	-521
chr19	44616806	44618482	E081	0
chr19	44644881	44646741	E081	27571
chr19	44575419	44575610	E082	-41700
chr19	44575642	44577153	E082	-40157
chr19	44598047	44599722	E082	-17588
chr19	44615925	44616789	E082	-521
chr19	44616806	44618482	E082	0
chr19	44644743	44644803	E082	27433
chr19	44644881	44646741	E082	27571