rs10963462

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

ADAMTSL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0148 (4450/29950,GnomAD)
T=0146 (4261/29118,TOPMED)
T=0136 (680/5008,1000G)
T=0203 (781/3854,ALSPAC)
T=0203 (753/3708,TWINSUK)

Position: chr9:18130038 (GRCh38.p7) (9p22.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 12 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.18130038G>T
GRCh37.p13 chr 9	NC_000009.11:g.18130036G>T

Gene: ADAMTSL1, ADAMTS like 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ADAMTSL1 transcript variant 4	NM_001040272.5:c.	N/A	Genic Upstream Transcript Variant
ADAMTSL1 transcript variant 2	NM_052866.4:c.	N/A	Genic Upstream Transcript Variant
ADAMTSL1 transcript variant X1	XM_011518063.2:c.	N/A	Intron Variant
ADAMTSL1 transcript variant X3	XM_011518064.2:c.	N/A	Intron Variant
ADAMTSL1 transcript variant X2	XM_017015310.1:c.	N/A	Intron Variant
ADAMTSL1 transcript variant X4	XM_017015311.1:c.	N/A	Intron Variant
ADAMTSL1 transcript variant X5	XM_017015312.1:c.	N/A	Intron Variant
ADAMTSL1 transcript variant X7	XM_017015314.1:c.	N/A	Intron Variant
ADAMTSL1 transcript variant X8	XM_011518067.1:c.	N/A	Genic Upstream Transcript Variant
ADAMTSL1 transcript variant X9	XM_011518068.2:c.	N/A	Genic Upstream Transcript Variant
ADAMTSL1 transcript variant X10	XM_011518070.2:c.	N/A	Genic Upstream Transcript Variant
ADAMTSL1 transcript variant X6	XM_017015313.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.966	T=0.034
1000Genomes	American	Sub	694	G=0.870	T=0.130
1000Genomes	East Asian	Sub	1008	G=0.796	T=0.204
1000Genomes	Europe	Sub	1006	G=0.788	T=0.212
1000Genomes	Global	Study-wide	5008	G=0.864	T=0.136
1000Genomes	South Asian	Sub	978	G=0.870	T=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.797	T=0.203
The Genome Aggregation Database	African	Sub	8722	G=0.939	T=0.061
The Genome Aggregation Database	American	Sub	838	G=0.890	T=0.110
The Genome Aggregation Database	East Asian	Sub	1604	G=0.815	T=0.185
The Genome Aggregation Database	Europe	Sub	18484	G=0.813	T=0.186
The Genome Aggregation Database	Global	Study-wide	29950	G=0.851	T=0.148
The Genome Aggregation Database	Other	Sub	302	G=0.740	T=0.260
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.853	T=0.146
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.797	T=0.203

PMID	Title	Author	Journal
23089632	A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.	Wang JC	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs10963462	0.00000622	alcohol dependence	23089632
rs10963462	0.0000118	alcohol dependence	23089632

eQTL of rs10963462 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 rs10963462 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 )
chr9	18106512	18106596	E074	-23440
chr9	18106669	18106793	E074	-23243
chr9	18126928	18127002	E074	-3034
chr9	18127030	18127178	E074	-2858
chr9	18127194	18127300	E074	-2736
chr9	18127415	18127505	E074	-2531
chr9	18126928	18127002	E081	-3034
chr9	18127030	18127178	E081	-2858
chr9	18127194	18127300	E081	-2736
chr9	18127415	18127505	E081	-2531
chr9	18127556	18127809	E081	-2227
chr9	18106016	18106109	E082	-23927