rs9343977

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

BCKDHB : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0471 (13889/29434,GnomAD)
C==0447 (13017/29118,TOPMED)
C==0378 (1895/5008,1000G)
T=0496 (1913/3854,ALSPAC)
T=0489 (1815/3708,TWINSUK)

Position: chr6:80257284 (GRCh38.p7) (6q14.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.80257284C>G
GRCh38.p7 chr 6	NC_000006.12:g.80257284C>T
GRCh37.p13 chr 6	NC_000006.11:g.80967001C>G
GRCh37.p13 chr 6	NC_000006.11:g.80967001C>T
BCKDHB RefSeqGene	NG_009775.1:g.155658C>G
BCKDHB RefSeqGene	NG_009775.1:g.155658C>T

Gene: BCKDHB, branched chain keto acid dehydrogenase E1, beta polypeptide(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BCKDHB transcript variant 2	NM_000056.4:c.	N/A	Intron Variant
BCKDHB transcript variant 3	NM_001318975.1:c.	N/A	Intron Variant
BCKDHB transcript variant 1	NM_183050.3:c.	N/A	Intron Variant
BCKDHB transcript variant 4	NR_134945.1:n.	N/A	Intron Variant
BCKDHB transcript variant X2	XM_005248756.4:c.	N/A	Intron Variant
BCKDHB transcript variant X5	XM_011536023.2:c.	N/A	Intron Variant
BCKDHB transcript variant X7	XM_011536024.2:c.	N/A	Intron Variant
BCKDHB transcript variant X8	XM_011536025.2:c.	N/A	Intron Variant
BCKDHB transcript variant X9	XM_011536026.2:c.	N/A	Intron Variant
BCKDHB transcript variant X1	XR_001743546.1:n.	N/A	Intron Variant
BCKDHB transcript variant X3	XR_001743547.1:n.	N/A	Intron Variant
BCKDHB transcript variant X4	XR_001743548.1:n.	N/A	Intron Variant
BCKDHB transcript variant X6	XR_001743549.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.433	T=0.567
1000Genomes	American	Sub	694	C=0.340	T=0.660
1000Genomes	East Asian	Sub	1008	C=0.312	T=0.688
1000Genomes	Europe	Sub	1006	C=0.486	T=0.514
1000Genomes	Global	Study-wide	5008	C=0.378	T=0.622
1000Genomes	South Asian	Sub	978	C=0.290	T=0.710
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.504	T=0.496
The Genome Aggregation Database	African	Sub	8608	C=0.426	T=0.574
The Genome Aggregation Database	American	Sub	776	C=0.320	T=0.68,
The Genome Aggregation Database	East Asian	Sub	1616	C=0.309	T=0.691
The Genome Aggregation Database	Europe	Sub	18132	C=0.514	T=0.485
The Genome Aggregation Database	Global	Study-wide	29434	C=0.471	T=0.528
The Genome Aggregation Database	Other	Sub	302	C=0.460	T=0.54,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.447	T=0.553
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.511	T=0.489

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

P-Value

SNP ID	p-value	Traits	Study
rs9343977	0.00028	alcohol dependence(early age of onset)	20201924
rs9343977	0.00036	alcohol dependence	20201924

eQTL of rs9343977 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 rs9343977 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.