rs3746228

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ZNF460 : 3 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0221 (6638/29946,GnomAD)
A=0166 (4856/29118,TOPMED)
A=0170 (853/5008,1000G)
A=0263 (1015/3854,ALSPAC)
A=0266 (986/3708,TWINSUK)

Position: chr19:57292994 (GRCh38.p7) (19q13.43)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 67 Enhancers around

Promoter: 28 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.57292994G>A
GRCh37.p13 chr 19	NC_000019.9:g.57804362G>A

Gene: ZNF460, zinc finger protein 460(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF460 transcript variant 1	NM_006635.3:c.	N/A	3 Prime UTR Variant
ZNF460 transcript variant X1	XM_017026176.1:c.	N/A	3 Prime UTR Variant
ZNF460 transcript variant X2	XM_005258422.3:c.	N/A	3 Prime UTR Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.951	A=0.049
1000Genomes	American	Sub	694	G=0.710	A=0.290
1000Genomes	East Asian	Sub	1008	G=0.839	A=0.161
1000Genomes	Europe	Sub	1006	G=0.748	A=0.252
1000Genomes	Global	Study-wide	5008	G=0.830	A=0.170
1000Genomes	South Asian	Sub	978	G=0.830	A=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.737	A=0.263
The Genome Aggregation Database	African	Sub	8728	G=0.911	A=0.089
The Genome Aggregation Database	American	Sub	836	G=0.670	A=0.330
The Genome Aggregation Database	East Asian	Sub	1616	G=0.851	A=0.149
The Genome Aggregation Database	Europe	Sub	18464	G=0.713	A=0.286
The Genome Aggregation Database	Global	Study-wide	29946	G=0.778	A=0.221
The Genome Aggregation Database	Other	Sub	302	G=0.830	A=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.833	A=0.166
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.734	A=0.266

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs3746228	0.000974	alcohol dependence	21314694

eQTL of rs3746228 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 rs3746228 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	57793441	57794225	E067	-10137
chr19	57794232	57794319	E067	-10043
chr19	57794426	57794510	E067	-9852
chr19	57794599	57794919	E067	-9443
chr19	57795057	57795227	E067	-9135
chr19	57795326	57795399	E067	-8963
chr19	57795489	57795540	E067	-8822
chr19	57795711	57795821	E067	-8541
chr19	57795900	57796082	E067	-8280
chr19	57834070	57834300	E067	29708
chr19	57794232	57794319	E068	-10043
chr19	57794426	57794510	E068	-9852
chr19	57794599	57794919	E068	-9443
chr19	57795057	57795227	E068	-9135
chr19	57834070	57834300	E068	29708
chr19	57793441	57794225	E069	-10137
chr19	57795057	57795227	E069	-9135
chr19	57795326	57795399	E069	-8963
chr19	57795489	57795540	E069	-8822
chr19	57834070	57834300	E069	29708
chr19	57834345	57834401	E069	29983
chr19	57794232	57794319	E070	-10043
chr19	57834070	57834300	E070	29708
chr19	57834345	57834401	E070	29983
chr19	57793441	57794225	E071	-10137
chr19	57794232	57794319	E071	-10043
chr19	57794426	57794510	E071	-9852
chr19	57794599	57794919	E071	-9443
chr19	57795057	57795227	E071	-9135
chr19	57795326	57795399	E071	-8963
chr19	57795489	57795540	E071	-8822
chr19	57795711	57795821	E071	-8541
chr19	57795900	57796082	E071	-8280
chr19	57796388	57796644	E071	-7718
chr19	57813136	57814762	E071	8774
chr19	57834070	57834300	E071	29708
chr19	57834345	57834401	E071	29983
chr19	57794232	57794319	E072	-10043
chr19	57794426	57794510	E072	-9852
chr19	57794599	57794919	E072	-9443
chr19	57834070	57834300	E072	29708
chr19	57754465	57754545	E073	-49817
chr19	57794426	57794510	E073	-9852
chr19	57794599	57794919	E073	-9443
chr19	57795057	57795227	E073	-9135
chr19	57795326	57795399	E073	-8963
chr19	57795489	57795540	E073	-8822
chr19	57795711	57795821	E073	-8541
chr19	57795900	57796082	E073	-8280
chr19	57796388	57796644	E073	-7718
chr19	57834070	57834300	E073	29708
chr19	57834345	57834401	E073	29983
chr19	57793441	57794225	E074	-10137
chr19	57794232	57794319	E074	-10043
chr19	57794426	57794510	E074	-9852
chr19	57794599	57794919	E074	-9443
chr19	57795057	57795227	E074	-9135
chr19	57795326	57795399	E074	-8963
chr19	57795489	57795540	E074	-8822
chr19	57795711	57795821	E074	-8541
chr19	57795900	57796082	E074	-8280
chr19	57793441	57794225	E081	-10137
chr19	57834070	57834300	E081	29708
chr19	57793441	57794225	E082	-10137
chr19	57794232	57794319	E082	-10043
chr19	57834070	57834300	E082	29708
chr19	57834345	57834401	E082	29983

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	57790555	57792900	E067	-11462
chr19	57828856	57828910	E067	24494
chr19	57828911	57829235	E067	24549
chr19	57831163	57832958	E067	26801
chr19	57790555	57792900	E068	-11462
chr19	57828856	57828910	E068	24494
chr19	57828911	57829235	E068	24549
chr19	57831163	57832958	E068	26801
chr19	57790555	57792900	E069	-11462
chr19	57831163	57832958	E069	26801
chr19	57790555	57792900	E070	-11462
chr19	57831163	57832958	E070	26801
chr19	57790555	57792900	E071	-11462
chr19	57828856	57828910	E071	24494
chr19	57828911	57829235	E071	24549
chr19	57831163	57832958	E071	26801
chr19	57790555	57792900	E072	-11462
chr19	57831163	57832958	E072	26801
chr19	57790555	57792900	E073	-11462
chr19	57828856	57828910	E073	24494
chr19	57828911	57829235	E073	24549
chr19	57831163	57832958	E073	26801
chr19	57790555	57792900	E074	-11462
chr19	57831163	57832958	E074	26801
chr19	57790555	57792900	E081	-11462
chr19	57831163	57832958	E081	26801
chr19	57790555	57792900	E082	-11462
chr19	57831163	57832958	E082	26801