SNP Detail Info-rs11682521

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SLC39A10 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0397 (11792/29682,GnomAD)
G==0422 (12308/29118,TOPMED)
G==0494 (2473/5008,1000G)
G==0302 (1164/3854,ALSPAC)
G==0290 (1077/3708,TWINSUK)

Position: chr2:195652785 (GRCh38.p7) (2q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 27 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.195652785G>A
GRCh37.p13 chr 2	NC_000002.11:g.196517509G>A

Molecule type	Change	Amino acid[Codon]	SO Term
SLC39A10 transcript variant 1	NM_001127257.1:c.	N/A	Genic Upstream Transcript Variant
SLC39A10 transcript variant 2	NM_020342.2:c.	N/A	Genic Upstream Transcript Variant
SLC39A10 transcript variant X2	XM_011511504.2:c.	N/A	Intron Variant
SLC39A10 transcript variant X4	XM_011511505.2:c.	N/A	Intron Variant
SLC39A10 transcript variant X1	XM_005246689.4:c.	N/A	Genic Upstream Transcript Variant
SLC39A10 transcript variant X3	XM_011511506.2:c.	N/A	Genic Upstream Transcript Variant
SLC39A10 transcript variant X5	XM_011511507.2:c.	N/A	Genic Upstream Transcript Variant
SLC39A10 transcript variant X6	XM_017004522.1:c.	N/A	Genic Upstream Transcript Variant
SLC39A10 transcript variant X7	XM_017004523.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.508	A=0.492
1000Genomes	American	Sub	694	G=0.510	A=0.490
1000Genomes	East Asian	Sub	1008	G=0.660	A=0.340
1000Genomes	Europe	Sub	1006	G=0.301	A=0.699
1000Genomes	Global	Study-wide	5008	G=0.494	A=0.506
1000Genomes	South Asian	Sub	978	G=0.490	A=0.510
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.302	A=0.698
The Genome Aggregation Database	African	Sub	8640	G=0.488	A=0.512
The Genome Aggregation Database	American	Sub	834	G=0.510	A=0.490
The Genome Aggregation Database	East Asian	Sub	1602	G=0.695	A=0.305
The Genome Aggregation Database	Europe	Sub	18304	G=0.321	A=0.678
The Genome Aggregation Database	Global	Study-wide	29682	G=0.397	A=0.602
The Genome Aggregation Database	Other	Sub	302	G=0.490	A=0.510
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.422	A=0.577
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.290	A=0.710

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs11682521	0.00034	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:196517509	SLC39A10	ENSG00000196950.9	G>A	9.2991e-9	76808	Cerebellum

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	196530924	196531064	E067	13415
chr2	196531147	196531249	E067	13638
chr2	196552291	196552796	E067	34782
chr2	196531147	196531249	E068	13638
chr2	196551759	196551919	E068	34250
chr2	196552291	196552796	E068	34782
chr2	196532763	196532990	E069	15254
chr2	196530924	196531064	E070	13415
chr2	196531147	196531249	E070	13638
chr2	196551398	196551453	E070	33889
chr2	196551579	196551657	E070	34070
chr2	196551759	196551919	E070	34250
chr2	196552291	196552796	E070	34782
chr2	196532763	196532990	E071	15254
chr2	196552291	196552796	E071	34782
chr2	196530924	196531064	E073	13415
chr2	196531147	196531249	E073	13638
chr2	196530924	196531064	E074	13415
chr2	196531147	196531249	E074	13638
chr2	196477241	196478162	E081	-39347
chr2	196526812	196526862	E081	9303
chr2	196527010	196527154	E081	9501
chr2	196527701	196527853	E081	10192
chr2	196527862	196528001	E081	10353
chr2	196528041	196528150	E081	10532
chr2	196531147	196531249	E081	13638
chr2	196552291	196552796	E082	34782

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	196520779	196524508	E067	3270
chr2	196520779	196524508	E068	3270
chr2	196520779	196524508	E069	3270
chr2	196520779	196524508	E070	3270
chr2	196520779	196524508	E071	3270
chr2	196520779	196524508	E072	3270
chr2	196520779	196524508	E073	3270
chr2	196520779	196524508	E074	3270
chr2	196520779	196524508	E081	3270
chr2	196520779	196524508	E082	3270

rs11682521