rs10406335

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ZNF225 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0218 (6539/29918,GnomAD)
G==0244 (7127/29118,TOPMED)
G==0328 (1644/5008,1000G)
G==0115 (445/3854,ALSPAC)
G==0119 (443/3708,TWINSUK)

Position: chr19:44129800 (GRCh38.p7) (19q13.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 29 Enhancers around

Promoter: 60 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.44129800G>A
GRCh37.p13 chr 19	NC_000019.9:g.44633953G>A

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	Intron Variant
ZNF225 transcript variant 1	NM_013362.3:c.	N/A	Intron Variant
ZNF225 transcript variant X3	XM_005259223.3:c.	N/A	Intron Variant
ZNF225 transcript variant X1	XM_011527285.2:c.	N/A	Intron Variant
ZNF225 transcript variant X2	XM_011527286.2:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.375	A=0.625
1000Genomes	American	Sub	694	G=0.420	A=0.580
1000Genomes	East Asian	Sub	1008	G=0.496	A=0.504
1000Genomes	Europe	Sub	1006	G=0.130	A=0.870
1000Genomes	Global	Study-wide	5008	G=0.328	A=0.672
1000Genomes	South Asian	Sub	978	G=0.230	A=0.770
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.115	A=0.885
The Genome Aggregation Database	African	Sub	8688	G=0.328	A=0.672
The Genome Aggregation Database	American	Sub	836	G=0.440	A=0.560
The Genome Aggregation Database	East Asian	Sub	1612	G=0.457	A=0.543
The Genome Aggregation Database	Europe	Sub	18480	G=0.137	A=0.862
The Genome Aggregation Database	Global	Study-wide	29918	G=0.218	A=0.781
The Genome Aggregation Database	Other	Sub	302	G=0.130	A=0.870
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.244	A=0.755
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.119	A=0.881

PMID	Title	Author	Journal
18823527	A genome-wide association study for late-onset Alzheimer's disease using DNA pooling.	Abraham R	BMC Med Genomics
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
rs10406335	0.000144	alcohol consumption	23743675

eQTL of rs10406335 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 rs10406335 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	44670758	44670818	E067	36805
chr19	44670933	44671011	E067	36980
chr19	44671049	44671115	E067	37096
chr19	44618883	44619034	E068	-14919
chr19	44670758	44670818	E068	36805
chr19	44670933	44671011	E068	36980
chr19	44600148	44600194	E069	-33759
chr19	44600148	44600194	E070	-33759
chr19	44618883	44619034	E070	-14919
chr19	44619037	44619091	E070	-14862
chr19	44619125	44619165	E070	-14788
chr19	44670758	44670818	E070	36805
chr19	44670933	44671011	E070	36980
chr19	44671049	44671115	E070	37096
chr19	44671876	44671938	E070	37923
chr19	44618883	44619034	E071	-14919
chr19	44670758	44670818	E071	36805
chr19	44670758	44670818	E072	36805
chr19	44670933	44671011	E072	36980
chr19	44670758	44670818	E074	36805
chr19	44670933	44671011	E074	36980
chr19	44671876	44671938	E074	37923
chr19	44670758	44670818	E081	36805
chr19	44670933	44671011	E081	36980
chr19	44671049	44671115	E081	37096
chr19	44671876	44671938	E081	37923
chr19	44600816	44600930	E082	-33023
chr19	44670933	44671011	E082	36980
chr19	44671049	44671115	E082	37096

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	44598047	44599722	E067	-34231
chr19	44615925	44616789	E067	-17164
chr19	44616806	44618482	E067	-15471
chr19	44644881	44646741	E067	10928
chr19	44668498	44670041	E067	34545
chr19	44597812	44597885	E068	-36068
chr19	44597935	44597989	E068	-35964
chr19	44598047	44599722	E068	-34231
chr19	44615787	44615827	E068	-18126
chr19	44615925	44616789	E068	-17164
chr19	44616806	44618482	E068	-15471
chr19	44644743	44644803	E068	10790
chr19	44644881	44646741	E068	10928
chr19	44668498	44670041	E068	34545
chr19	44598047	44599722	E069	-34231
chr19	44615787	44615827	E069	-18126
chr19	44615925	44616789	E069	-17164
chr19	44616806	44618482	E069	-15471
chr19	44644881	44646741	E069	10928
chr19	44668498	44670041	E069	34545
chr19	44598047	44599722	E070	-34231
chr19	44615925	44616789	E070	-17164
chr19	44616806	44618482	E070	-15471
chr19	44644743	44644803	E070	10790
chr19	44644881	44646741	E070	10928
chr19	44668498	44670041	E070	34545
chr19	44598047	44599722	E071	-34231
chr19	44615787	44615827	E071	-18126
chr19	44615925	44616789	E071	-17164
chr19	44616806	44618482	E071	-15471
chr19	44644743	44644803	E071	10790
chr19	44644881	44646741	E071	10928
chr19	44668498	44670041	E071	34545
chr19	44598047	44599722	E072	-34231
chr19	44615925	44616789	E072	-17164
chr19	44616806	44618482	E072	-15471
chr19	44644743	44644803	E072	10790
chr19	44644881	44646741	E072	10928
chr19	44668498	44670041	E072	34545
chr19	44598047	44599722	E073	-34231
chr19	44615925	44616789	E073	-17164
chr19	44616806	44618482	E073	-15471
chr19	44644881	44646741	E073	10928
chr19	44668498	44670041	E073	34545
chr19	44598047	44599722	E074	-34231
chr19	44615925	44616789	E074	-17164
chr19	44616806	44618482	E074	-15471
chr19	44644881	44646741	E074	10928
chr19	44668498	44670041	E074	34545
chr19	44598047	44599722	E081	-34231
chr19	44615925	44616789	E081	-17164
chr19	44616806	44618482	E081	-15471
chr19	44644881	44646741	E081	10928
chr19	44668498	44670041	E081	34545
chr19	44598047	44599722	E082	-34231
chr19	44615925	44616789	E082	-17164
chr19	44616806	44618482	E082	-15471
chr19	44644743	44644803	E082	10790
chr19	44644881	44646741	E082	10928
chr19	44668498	44670041	E082	34545