SNP Detail Info-rs13295927

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SHC3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0106 (3200/29924,GnomAD)
C=0093 (2714/29118,TOPMED)
C=0061 (307/5008,1000G)
C=0178 (686/3854,ALSPAC)
C=0174 (646/3708,TWINSUK)

Position: chr9:89117794 (GRCh38.p7) (9q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 26 Enhancers around

Promoter: 4 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.89117794T>C
GRCh37.p13 chr 9	NC_000009.11:g.91732709T>C

Molecule type	Change	Amino acid[Codon]	SO Term
SHC3 transcript	NM_016848.5:c.	N/A	Intron Variant
SHC3 transcript variant X1	XM_011518785.2:c.	N/A	Intron Variant
SHC3 transcript variant X3	XM_017014809.1:c.	N/A	Intron Variant
SHC3 transcript variant X4	XM_017014810.1:c.	N/A	Intron Variant
SHC3 transcript variant X2	XM_011518786.2:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.997	C=0.003
1000Genomes	American	Sub	694	T=0.920	C=0.080
1000Genomes	East Asian	Sub	1008	T=0.988	C=0.012
1000Genomes	Europe	Sub	1006	T=0.848	C=0.152
1000Genomes	Global	Study-wide	5008	T=0.939	C=0.061
1000Genomes	South Asian	Sub	978	T=0.920	C=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.822	C=0.178
The Genome Aggregation Database	African	Sub	8730	T=0.971	C=0.029
The Genome Aggregation Database	American	Sub	838	T=0.940	C=0.060
The Genome Aggregation Database	East Asian	Sub	1612	T=0.989	C=0.011
The Genome Aggregation Database	Europe	Sub	18442	T=0.845	C=0.154
The Genome Aggregation Database	Global	Study-wide	29924	T=0.893	C=0.106
The Genome Aggregation Database	Other	Sub	302	T=0.900	C=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.906	C=0.093
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.826	C=0.174

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
rs13295927	0.0000063	alcohol dependence	20201924
rs13295927	0.00000631	alcoholism	pha002893
rs13295927	0.00043	alcohol dependence(early age of onset)	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr9	91692795	91693049	E067	-39660
chr9	91693182	91693282	E067	-39427
chr9	91693368	91693431	E067	-39278
chr9	91693537	91693729	E067	-38980
chr9	91694278	91695531	E067	-37178
chr9	91752586	91753179	E067	19877
chr9	91694278	91695531	E068	-37178
chr9	91769236	91770012	E068	36527
chr9	91770046	91770096	E068	37337
chr9	91694278	91695531	E069	-37178
chr9	91768234	91769019	E069	35525
chr9	91694278	91695531	E071	-37178
chr9	91752586	91753179	E072	19877
chr9	91768234	91769019	E072	35525
chr9	91692795	91693049	E073	-39660
chr9	91693182	91693282	E073	-39427
chr9	91693368	91693431	E073	-39278
chr9	91693537	91693729	E073	-38980
chr9	91694278	91695531	E073	-37178
chr9	91752586	91753179	E073	19877
chr9	91726748	91726843	E081	-5866
chr9	91726957	91727144	E081	-5565
chr9	91727203	91727354	E081	-5355
chr9	91727469	91727537	E081	-5172
chr9	91775804	91775863	E082	43095
chr9	91775891	91776003	E082	43182

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	91760092	91760358	E069	27383
chr9	91760092	91760358	E071	27383
chr9	91760092	91760358	E072	27383
chr9	91760092	91760358	E073	27383

rs13295927