rs2052603

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

ANO6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0163 (4878/29822,GnomAD)
T=0195 (5703/29118,TOPMED)
T=0248 (1244/5008,1000G)
T=0065 (251/3854,ALSPAC)
T=0068 (252/3708,TWINSUK)

Position: chr12:45252483 (GRCh38.p7) (12q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.45252483G>T
GRCh37.p13 chr 12	NC_000012.11:g.45646266G>T
ANO6 RefSeqGene	NG_028220.1:g.41497G>T

Gene: ANO6, anoctamin 6(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ANO6 transcript variant 1	NM_001025356.2:c.	N/A	Intron Variant
ANO6 transcript variant 3	NM_001142679.1:c.	N/A	Intron Variant
ANO6 transcript variant 5	NM_001204803.1:c.	N/A	Intron Variant
ANO6 transcript variant 2	NM_001142678.1:c.	N/A	Genic Upstream Transcript Variant
ANO6 transcript variant X2	XM_005268707.3:c.	N/A	Intron Variant
ANO6 transcript variant X1	XM_005268706.4:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.619	T=0.381
1000Genomes	American	Sub	694	G=0.870	T=0.130
1000Genomes	East Asian	Sub	1008	G=0.634	T=0.366
1000Genomes	Europe	Sub	1006	G=0.936	T=0.064
1000Genomes	Global	Study-wide	5008	G=0.752	T=0.248
1000Genomes	South Asian	Sub	978	G=0.780	T=0.220
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.935	T=0.065
The Genome Aggregation Database	African	Sub	8710	G=0.660	T=0.340
The Genome Aggregation Database	American	Sub	836	G=0.880	T=0.120
The Genome Aggregation Database	East Asian	Sub	1600	G=0.639	T=0.361
The Genome Aggregation Database	Europe	Sub	18374	G=0.933	T=0.066
The Genome Aggregation Database	Global	Study-wide	29822	G=0.836	T=0.163
The Genome Aggregation Database	Other	Sub	302	G=0.920	T=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.804	T=0.195
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.932	T=0.068

PMID	Title	Author	Journal
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs2052603	2.23E-05	alcohol dependence	19581569

eQTL of rs2052603 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 rs2052603 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 )
chr12	45627842	45629879	E067	-16387
chr12	45653291	45654710	E067	7025
chr12	45613039	45613097	E068	-33169
chr12	45613140	45613282	E068	-32984
chr12	45613323	45613527	E068	-32739
chr12	45613540	45613906	E068	-32360
chr12	45613911	45614629	E068	-31637
chr12	45621175	45621790	E068	-24476
chr12	45625376	45627217	E068	-19049
chr12	45627842	45629879	E068	-16387
chr12	45617806	45618044	E069	-28222
chr12	45627842	45629879	E069	-16387
chr12	45612211	45612285	E070	-33981
chr12	45612367	45612435	E070	-33831
chr12	45621175	45621790	E070	-24476
chr12	45621886	45622061	E070	-24205
chr12	45622282	45622342	E070	-23924
chr12	45650673	45650791	E070	4407
chr12	45677825	45678656	E070	31559
chr12	45678720	45678770	E070	32454
chr12	45612211	45612285	E071	-33981
chr12	45612367	45612435	E071	-33831
chr12	45613911	45614629	E071	-31637
chr12	45627842	45629879	E071	-16387
chr12	45650845	45651677	E071	4579
chr12	45652896	45653007	E071	6630
chr12	45653114	45653222	E071	6848
chr12	45653291	45654710	E071	7025
chr12	45612211	45612285	E072	-33981
chr12	45612367	45612435	E072	-33831
chr12	45627842	45629879	E072	-16387
chr12	45612211	45612285	E073	-33981
chr12	45612367	45612435	E073	-33831
chr12	45625376	45627217	E073	-19049
chr12	45627842	45629879	E073	-16387
chr12	45650845	45651677	E073	4579
chr12	45653114	45653222	E073	6848
chr12	45653291	45654710	E073	7025
chr12	45662345	45663376	E073	16079
chr12	45613540	45613906	E074	-32360
chr12	45625376	45627217	E074	-19049
chr12	45627218	45627433	E074	-18833
chr12	45642810	45642850	E074	-3416
chr12	45650845	45651677	E074	4579
chr12	45667381	45668266	E074	21115
chr12	45694607	45694683	E074	48341
chr12	45694736	45694846	E074	48470
chr12	45650845	45651677	E081	4579
chr12	45651904	45651954	E081	5638
chr12	45652366	45652434	E081	6100
chr12	45652604	45652702	E081	6338
chr12	45652896	45653007	E081	6630
chr12	45653114	45653222	E081	6848
chr12	45673707	45674240	E081	27441
chr12	45674311	45674566	E081	28045
chr12	45653114	45653222	E082	6848
chr12	45653291	45654710	E082	7025

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	45608432	45611905	E067	-34361
chr12	45608432	45611905	E068	-34361
chr12	45608432	45611905	E069	-34361
chr12	45608432	45611905	E070	-34361
chr12	45608432	45611905	E071	-34361
chr12	45608432	45611905	E072	-34361
chr12	45608432	45611905	E073	-34361
chr12	45608432	45611905	E074	-34361
chr12	45608432	45611905	E081	-34361
chr12	45608432	45611905	E082	-34361