rs62392942

Homo sapiens
T>C
GABBR1 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0048 (1457/29952,GnomAD)
C=0045 (1312/29118,TOPMED)
C=0057 (286/5008,1000G)
C=0053 (204/3854,ALSPAC)
C=0054 (202/3708,TWINSUK)
chr6:29634161 (GRCh38.p7) (6p22.1)
ND
GWASCatalog
1   publication(s)
See rs on genome
133 Enhancers around
127 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.29634161T>C
GRCh37.p13 chr 6NC_000006.11:g.29601938T>C
GABBR1 RefSeqGeneNG_029101.1:g.4025A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.1120634T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.1120740T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.899709T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.905294T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.899548T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.905133T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.899664T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.905260T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.2:g.899872T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.1:g.905466T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.943195T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.942493T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.899280T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.904900T>C

Gene: GABBR1, gamma-aminobutyric acid type B receptor subunit 1(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
GABBR1 transcript variant 5NM_001319053.1:c.N/AUpstream Transcript Variant
GABBR1 transcript variant 1NM_001470.3:c.N/AUpstream Transcript Variant
GABBR1 transcript variant 3NM_021904.3:c.N/AUpstream Transcript Variant
GABBR1 transcript variant 2NM_021903.2:c.N/AN/A
GABBR1 transcript variant X1XM_005248982.2:c.N/AUpstream Transcript Variant
GABBR1 transcript variant X2XM_006715047.3:c.N/AUpstream Transcript Variant
GABBR1 transcript variant X3XM_011514453.2:c.N/AUpstream Transcript Variant
GABBR1 transcript variant X5XM_011514455.1:c.N/AUpstream Transcript Variant
GABBR1 transcript variant X4XM_017010676.1:c.N/AUpstream Transcript Variant
GABBR1 transcript variant X6XR_001743302.1:n.N/AUpstream Transcript Variant
GABBR1 transcript variant X7XR_001743303.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.974C=0.026
1000GenomesAmericanSub694T=0.960C=0.040
1000GenomesEast AsianSub1008T=0.890C=0.110
1000GenomesEuropeSub1006T=0.950C=0.050
1000GenomesGlobalStudy-wide5008T=0.943C=0.057
1000GenomesSouth AsianSub978T=0.930C=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.947C=0.053
The Genome Aggregation DatabaseAfricanSub8726T=0.974C=0.026
The Genome Aggregation DatabaseAmericanSub836T=0.970C=0.030
The Genome Aggregation DatabaseEast AsianSub1620T=0.846C=0.154
The Genome Aggregation DatabaseEuropeSub18468T=0.948C=0.051
The Genome Aggregation DatabaseGlobalStudy-wide29952T=0.951C=0.048
The Genome Aggregation DatabaseOtherSub302T=0.970C=0.030
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.954C=0.045
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.946C=0.054
PMID Title Author Journal
28440896Genome-wide meta-analysis identifies a novel susceptibility signal at CACNA2D3 for nicotine dependence.Yin XAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs623929421E-06nicotine dependence28440896

eQTL of rs62392942 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:29601938GABBR1ENSG00000204681.6T>C1.2854e-8185Cerebellum
Chr6:29601938GABBR1ENSG00000204681.6T>C5.3597e-4185Cerebellar_Hemisphere

meQTL of rs62392942 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 )
chr62957605929576215E067-25723
chr62959086529590950E067-10988
chr62959107629591182E067-10756
chr62962080629621208E06718868
chr62962122229621509E06719284
chr62962186029622016E06719922
chr62962226229622302E06720324
chr62962282629623241E06720888
chr62962336229624255E06721424
chr62963028929630395E06728351
chr62963047929630577E06728541
chr62963362729634063E06731689
chr62963415729634383E06732219
chr62956181629561914E068-40024
chr62957181029571924E068-30014
chr62957218729572252E068-29686
chr62957265529572814E068-29124
chr62957299329573078E068-28860
chr62957605929576215E068-25723
chr62958100429581054E068-20884
chr62958109229581372E068-20566
chr62959168129592705E068-9233
chr62962186029622016E06819922
chr62962226229622302E06820324
chr62962282629623241E06820888
chr62963362729634063E06831689
chr62963415729634383E06832219
chr62957073229570799E069-31139
chr62957086929571058E069-30880
chr62957119529571304E069-30634
chr62957181029571924E069-30014
chr62957218729572252E069-29686
chr62957605929576215E069-25723
chr62959015229590271E069-11667
chr62959043729590525E069-11413
chr62959086529590950E069-10988
chr62959107629591182E069-10756
chr62959168129592705E069-9233
chr62960197229602095E06934
chr62960215329602208E069215
chr62960229629602597E069358
chr62962186029622016E06919922
chr62962226229622302E06920324
chr62962282629623241E06920888
chr62962336229624255E06921424
chr62963123129631471E06929293
chr62963148829631807E06929550
chr62963362729634063E06931689
chr62963415729634383E06932219
chr62963446629635320E06932528
chr62957086929571058E070-30880
chr62957119529571304E070-30634
chr62957181029571924E070-30014
chr62957218729572252E070-29686
chr62958849729588657E070-13281
chr62959812029598170E070-3768
chr62959845629598506E070-3432
chr62959865129598705E070-3233
chr62957265529572814E071-29124
chr62957299329573078E071-28860
chr62957605929576215E071-25723
chr62957901029579131E071-22807
chr62959015229590271E071-11667
chr62959043729590525E071-11413
chr62961930729619761E07117369
chr62961999529620159E07118057
chr62962018929620249E07118251
chr62962080629621208E07118868
chr62962122229621509E07119284
chr62962186029622016E07119922
chr62962226229622302E07120324
chr62962282629623241E07120888
chr62963148829631807E07129550
chr62963187729631934E07129939
chr62963231529632365E07130377
chr62963362729634063E07131689
chr62963415729634383E07132219
chr62963446629635320E07132528
chr62957605929576215E072-25723
chr62959015229590271E072-11667
chr62959043729590525E072-11413
chr62959749129597587E072-4351
chr62962122229621509E07219284
chr62962186029622016E07219922
chr62962226229622302E07220324
chr62962336229624255E07221424
chr62963123129631471E07229293
chr62963148829631807E07229550
chr62963187729631934E07229939
chr62963362729634063E07231689
chr62963415729634383E07232219
chr62963446629635320E07232528
chr62957119529571304E073-30634
chr62957181029571924E073-30014
chr62957218729572252E073-29686
chr62958034829580431E073-21507
chr62958849729588657E073-13281
chr62959015229590271E073-11667
chr62959043729590525E073-11413
chr62959086529590950E073-10988
chr62959107629591182E073-10756
chr62959168129592705E073-9233
chr62959749129597587E073-4351
chr62959812029598170E073-3768
chr62959845629598506E073-3432
chr62959865129598705E073-3233
chr62960197229602095E07334
chr62960215329602208E073215
chr62960229629602597E073358
chr62961930729619761E07317369
chr62962186029622016E07319922
chr62959107629591182E074-10756
chr62962080629621208E07418868
chr62962122229621509E07419284
chr62962186029622016E07419922
chr62962226229622302E07420324
chr62962282629623241E07420888
chr62962336229624255E07421424
chr62963338429633535E07431446
chr62963362729634063E07431689
chr62963415729634383E07432219
chr62963446629635320E07432528
chr62963547529635581E07433537
chr62957119529571304E081-30634
chr62959749129597587E081-4351
chr62959812029598170E081-3768
chr62959845629598506E081-3432
chr62959865129598705E081-3233
chr62960215329602208E081215
chr62960229629602597E081358
chr62957181029571924E082-30014
chr62957218729572252E082-29686
chr62959168129592705E082-9233










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr62959273229593051E067-8887
chr62959320129593355E067-8583
chr62959359529593846E067-8092
chr62959400629594128E067-7810
chr62959416329594272E067-7666
chr62959438729594603E067-7335
chr62959464829594713E067-7225
chr62959475429595087E067-6851
chr62959512529597042E067-4896
chr62959971429601810E067-128
chr62961727729618468E06715339
chr62962499229625042E06723054
chr62962600529626128E06724067
chr62962768629627740E06725748
chr62962935129629494E06727413
chr62959273229593051E068-8887
chr62959320129593355E068-8583
chr62959359529593846E068-8092
chr62959400629594128E068-7810
chr62959416329594272E068-7666
chr62959438729594603E068-7335
chr62959464829594713E068-7225
chr62959475429595087E068-6851
chr62959512529597042E068-4896
chr62959971429601810E068-128
chr62961727729618468E06815339
chr62962499229625042E06823054
chr62962600529626128E06824067
chr62962768629627740E06825748
chr62962935129629494E06827413
chr62959273229593051E069-8887
chr62959320129593355E069-8583
chr62959359529593846E069-8092
chr62959400629594128E069-7810
chr62959416329594272E069-7666
chr62959438729594603E069-7335
chr62959464829594713E069-7225
chr62959475429595087E069-6851
chr62959512529597042E069-4896
chr62959971429601810E069-128
chr62961727729618468E06915339
chr62962499229625042E06923054
chr62962600529626128E06924067
chr62962768629627740E06925748
chr62962935129629494E06927413
chr62959273229593051E070-8887
chr62959320129593355E070-8583
chr62959359529593846E070-8092
chr62959400629594128E070-7810
chr62959416329594272E070-7666
chr62959438729594603E070-7335
chr62959464829594713E070-7225
chr62959475429595087E070-6851
chr62959512529597042E070-4896
chr62959971429601810E070-128
chr62961727729618468E07015339
chr62959273229593051E071-8887
chr62959320129593355E071-8583
chr62959359529593846E071-8092
chr62959400629594128E071-7810
chr62959416329594272E071-7666
chr62959438729594603E071-7335
chr62959464829594713E071-7225
chr62959475429595087E071-6851
chr62959512529597042E071-4896
chr62959971429601810E071-128
chr62961727729618468E07115339
chr62962499229625042E07123054
chr62962600529626128E07124067
chr62962935129629494E07127413
chr62959273229593051E072-8887
chr62959320129593355E072-8583
chr62959359529593846E072-8092
chr62959400629594128E072-7810
chr62959416329594272E072-7666
chr62959438729594603E072-7335
chr62959464829594713E072-7225
chr62959475429595087E072-6851
chr62959512529597042E072-4896
chr62959971429601810E072-128
chr62961727729618468E07215339
chr62962499229625042E07223054
chr62962600529626128E07224067
chr62962768629627740E07225748
chr62959273229593051E073-8887
chr62959320129593355E073-8583
chr62959359529593846E073-8092
chr62959400629594128E073-7810
chr62959416329594272E073-7666
chr62959438729594603E073-7335
chr62959464829594713E073-7225
chr62959475429595087E073-6851
chr62959512529597042E073-4896
chr62959971429601810E073-128
chr62961727729618468E07315339
chr62962499229625042E07323054
chr62962600529626128E07324067
chr62962768629627740E07325748
chr62959359529593846E074-8092
chr62959400629594128E074-7810
chr62959416329594272E074-7666
chr62959438729594603E074-7335
chr62959464829594713E074-7225
chr62959475429595087E074-6851
chr62959512529597042E074-4896
chr62959971429601810E074-128
chr62961727729618468E07415339
chr62962499229625042E07423054
chr62962600529626128E07424067
chr62962768629627740E07425748
chr62962935129629494E07427413
chr62959438729594603E081-7335
chr62959464829594713E081-7225
chr62959475429595087E081-6851
chr62959971429601810E081-128
chr62961727729618468E08115339
chr62959273229593051E082-8887
chr62959320129593355E082-8583
chr62959359529593846E082-8092
chr62959400629594128E082-7810
chr62959416329594272E082-7666
chr62959438729594603E082-7335
chr62959464829594713E082-7225
chr62959475429595087E082-6851
chr62959512529597042E082-4896
chr62959971429601810E082-128
chr62961727729618468E08215339