rs3812121

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

BCKDHB : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0363 (10876/29912,GnomAD)
G=0324 (9434/29118,TOPMED)
G=0395 (1980/5008,1000G)
G=0450 (1735/3854,ALSPAC)
G=0436 (1617/3708,TWINSUK)

Position: chr6:80259010 (GRCh38.p7) (6q14.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 17 Enhancers 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.80259010A>G
GRCh37.p13 chr 6	NC_000006.11:g.80968727A>G
BCKDHB RefSeqGene	NG_009775.1:g.157384A>G

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	A=0.907	G=0.093
1000Genomes	American	Sub	694	A=0.380	G=0.620
1000Genomes	East Asian	Sub	1008	A=0.444	G=0.556
1000Genomes	Europe	Sub	1006	A=0.543	G=0.457
1000Genomes	Global	Study-wide	5008	A=0.605	G=0.395
1000Genomes	South Asian	Sub	978	A=0.580	G=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.550	G=0.450
The Genome Aggregation Database	African	Sub	8706	A=0.852	G=0.148
The Genome Aggregation Database	American	Sub	836	A=0.380	G=0.620
The Genome Aggregation Database	East Asian	Sub	1606	A=0.439	G=0.561
The Genome Aggregation Database	Europe	Sub	18462	A=0.565	G=0.434
The Genome Aggregation Database	Global	Study-wide	29912	A=0.636	G=0.363
The Genome Aggregation Database	Other	Sub	302	A=0.510	G=0.490
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.676	G=0.324
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.564	G=0.436

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
rs3812121	0.0000207	alcoholism	pha002893
rs3812121	0.000021	alcohol dependence	20201924
rs3812121	0.00004	alcohol dependence(early age of onset)	20201924
rs3812121	0.0000403	alcoholism	pha002892

eQTL of rs3812121 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 rs3812121 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 )
chr6	80964352	80964402	E067	-4325
chr6	80964487	80964643	E067	-4084
chr6	80978330	80978551	E067	9603
chr6	80978966	80979066	E067	10239
chr6	80977692	80977816	E068	8965
chr6	80956829	80957013	E071	-11714
chr6	80957369	80957551	E071	-11176
chr6	80964352	80964402	E071	-4325
chr6	80964487	80964643	E071	-4084
chr6	80964352	80964402	E072	-4325
chr6	80964487	80964643	E072	-4084
chr6	80956829	80957013	E074	-11714
chr6	80957369	80957551	E074	-11176
chr6	80964352	80964402	E074	-4325
chr6	80978330	80978551	E074	9603
chr6	80986310	80986364	E082	17583
chr6	80986677	80986794	E082	17950