SNP Detail Info-rs12662682

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

KCNQ5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0052 (1566/29976,GnomAD)
G=0055 (1625/29118,TOPMED)
G=0056 (280/5008,1000G)
G=0038 (147/3854,ALSPAC)
G=0043 (161/3708,TWINSUK)

Position: chr6:73180074 (GRCh38.p7) (6q13)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 5 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.73180074A>G
GRCh37.p13 chr 6	NC_000006.11:g.73889797A>G

Molecule type	Change	Amino acid[Codon]	SO Term
KCNQ5 transcript variant 2	NM_001160130.1:c.	N/A	Intron Variant
KCNQ5 transcript variant 3	NM_001160132.1:c.	N/A	Intron Variant
KCNQ5 transcript variant 4	NM_001160133.1:c.	N/A	Intron Variant
KCNQ5 transcript variant 5	NM_001160134.1:c.	N/A	Intron Variant
KCNQ5 transcript variant 1	NM_019842.3:c.	N/A	Intron Variant
KCNQ5 transcript variant X1	XM_017011058.1:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.911	G=0.089
1000Genomes	American	Sub	694	A=0.980	G=0.020
1000Genomes	East Asian	Sub	1008	A=0.914	G=0.086
1000Genomes	Europe	Sub	1006	A=0.969	G=0.031
1000Genomes	Global	Study-wide	5008	A=0.944	G=0.056
1000Genomes	South Asian	Sub	978	A=0.970	G=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.962	G=0.038
The Genome Aggregation Database	African	Sub	8732	A=0.925	G=0.075
The Genome Aggregation Database	American	Sub	838	A=0.980	G=0.020
The Genome Aggregation Database	East Asian	Sub	1618	A=0.885	G=0.115
The Genome Aggregation Database	Europe	Sub	18486	A=0.962	G=0.037
The Genome Aggregation Database	Global	Study-wide	29976	A=0.947	G=0.052
The Genome Aggregation Database	Other	Sub	302	A=0.990	G=0.010
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.944	G=0.055
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.957	G=0.043

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

SNP ID	p-value	Traits	Study
rs12662682	2.81E-05	alcohol dependence	21314694

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 )
chr6	73854425	73854475	E068	-35322
chr6	73889933	73890139	E069	136
chr6	73890151	73890327	E069	354
chr6	73890151	73890327	E072	354
chr6	73889933	73890139	E073	136
chr6	73890151	73890327	E073	354
chr6	73861552	73861711	E081	-28086
chr6	73862733	73863359	E081	-26438

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr6	73890426	73891185	E067	629
chr6	73890426	73891185	E068	629
chr6	73890426	73891185	E072	629
chr6	73890426	73891185	E073	629
chr6	73890426	73891185	E074	629

rs12662682