rs2179842

Homo sapiens
T>C
BCKDHB : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0377 (11294/29914,GnomAD)
C=0342 (9968/29118,TOPMED)
C=0409 (2050/5008,1000G)
C=0450 (1736/3854,ALSPAC)
C=0436 (1618/3708,TWINSUK)
chr6:80269336 (GRCh38.p7) (6q14.1)
AD
GWASdb2
1   publication(s)
See rs on genome
20 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.80269336T>C
GRCh37.p13 chr 6NC_000006.11:g.80979053T>C
BCKDHB RefSeqGeneNG_009775.1:g.167710T>C

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

Molecule type Change Amino acid[Codon] SO Term
BCKDHB transcript variant 2NM_000056.4:c.N/AIntron Variant
BCKDHB transcript variant 3NM_001318975.1:c.N/AIntron Variant
BCKDHB transcript variant 1NM_183050.3:c.N/AIntron Variant
BCKDHB transcript variant 4NR_134945.1:n.N/AIntron Variant
BCKDHB transcript variant X2XM_005248756.4:c.N/AIntron Variant
BCKDHB transcript variant X5XM_011536023.2:c.N/AIntron Variant
BCKDHB transcript variant X7XM_011536024.2:c.N/AIntron Variant
BCKDHB transcript variant X8XM_011536025.2:c.N/AIntron Variant
BCKDHB transcript variant X9XM_011536026.2:c.N/AIntron Variant
BCKDHB transcript variant X1XR_001743546.1:n.N/AIntron Variant
BCKDHB transcript variant X3XR_001743547.1:n.N/AIntron Variant
BCKDHB transcript variant X4XR_001743548.1:n.N/AIntron Variant
BCKDHB transcript variant X6XR_001743549.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.856C=0.144
1000GenomesAmericanSub694T=0.380C=0.620
1000GenomesEast AsianSub1008T=0.445C=0.555
1000GenomesEuropeSub1006T=0.542C=0.458
1000GenomesGlobalStudy-wide5008T=0.591C=0.409
1000GenomesSouth AsianSub978T=0.580C=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.550C=0.450
The Genome Aggregation DatabaseAfricanSub8720T=0.807C=0.193
The Genome Aggregation DatabaseAmericanSub836T=0.380C=0.620
The Genome Aggregation DatabaseEast AsianSub1592T=0.439C=0.561
The Genome Aggregation DatabaseEuropeSub18464T=0.563C=0.436
The Genome Aggregation DatabaseGlobalStudy-wide29914T=0.622C=0.377
The Genome Aggregation DatabaseOtherSub302T=0.520C=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.657C=0.342
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.564C=0.436
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs21798420.000026alcohol dependence20201924
rs21798420.0000261alcoholismpha002893
rs21798420.000035alcohol dependence(early age of onset)20201924
rs21798420.0000351alcoholismpha002892

eQTL of rs2179842 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:80979053RP11-250B2.5ENSG00000260645.1T>C4.8851e-3-197622Cerebellum
Chr6:80979053RP11-250B2.3ENSG00000233967.2T>C2.0264e-2-174008Cerebellar_Hemisphere

meQTL of rs2179842 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 )
chr68096435280964402E067-14651
chr68096448780964643E067-14410
chr68097833080978551E067-502
chr68097896680979066E0670
chr68097769280977816E068-1237
chr68102628681026914E06847233
chr68095682980957013E071-22040
chr68095736980957551E071-21502
chr68096435280964402E071-14651
chr68096448780964643E071-14410
chr68102628681026914E07147233
chr68096435280964402E072-14651
chr68096448780964643E072-14410
chr68102628681026914E07247233
chr68095682980957013E074-22040
chr68095736980957551E074-21502
chr68096435280964402E074-14651
chr68097833080978551E074-502
chr68098631080986364E0827257
chr68098667780986794E0827624