rs56020557

Homo sapiens
C>T
None
Check p-value
SNV (Single Nucleotide Variation)
T=0056 (1700/29928,GnomAD)
T=0053 (1549/29118,TOPMED)
T=0080 (400/5008,1000G)
T=0058 (223/3854,ALSPAC)
T=0061 (228/3708,TWINSUK)
chr6:29596985 (GRCh38.p7) (6p22.1)
ND
GWASCatalog
1   publication(s)
See rs on genome
72 Enhancers around
106 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.29596985C>T
GRCh37.p13 chr 6NC_000006.11:g.29564762C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.1083465C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.1083571C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.862497C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.868093C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.862534C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.868119C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.862166C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.867786C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.862380C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.867965C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.2:g.862710C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.1:g.868304C>T

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.952T=0.048
1000GenomesAmericanSub694C=0.960T=0.040
1000GenomesEast AsianSub1008C=0.879T=0.121
1000GenomesEuropeSub1006C=0.948T=0.052
1000GenomesGlobalStudy-wide5008C=0.920T=0.080
1000GenomesSouth AsianSub978C=0.870T=0.130
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.942T=0.058
The Genome Aggregation DatabaseAfricanSub8710C=0.960T=0.040
The Genome Aggregation DatabaseAmericanSub832C=0.970T=0.030
The Genome Aggregation DatabaseEast AsianSub1616C=0.838T=0.162
The Genome Aggregation DatabaseEuropeSub18468C=0.943T=0.056
The Genome Aggregation DatabaseGlobalStudy-wide29928C=0.943T=0.056
The Genome Aggregation DatabaseOtherSub302C=0.950T=0.050
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.946T=0.053
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.939T=0.061
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
rs560205575E-06nicotine dependence28440896

eQTL of rs56020557 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:29564762GABBR1ENSG00000204681.6C>T1.2854e-8-36991Cerebellum
Chr6:29564762GABBR1ENSG00000204681.6C>T5.3597e-4-36991Cerebellar_Hemisphere

meQTL of rs56020557 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 )
chr62957605929576215E06711297
chr62959086529590950E06726103
chr62959107629591182E06726314
chr62956181629561914E068-2848
chr62957181029571924E0687048
chr62957218729572252E0687425
chr62957265529572814E0687893
chr62957299329573078E0688231
chr62957605929576215E06811297
chr62958100429581054E06816242
chr62958109229581372E06816330
chr62959168129592705E06826919
chr62957073229570799E0695970
chr62957086929571058E0696107
chr62957119529571304E0696433
chr62957181029571924E0697048
chr62957218729572252E0697425
chr62957605929576215E06911297
chr62959015229590271E06925390
chr62959043729590525E06925675
chr62959086529590950E06926103
chr62959107629591182E06926314
chr62959168129592705E06926919
chr62960197229602095E06937210
chr62960215329602208E06937391
chr62960229629602597E06937534
chr62957086929571058E0706107
chr62957119529571304E0706433
chr62957181029571924E0707048
chr62957218729572252E0707425
chr62958849729588657E07023735
chr62959812029598170E07033358
chr62959845629598506E07033694
chr62959865129598705E07033889
chr62957265529572814E0717893
chr62957299329573078E0718231
chr62957605929576215E07111297
chr62957901029579131E07114248
chr62959015229590271E07125390
chr62959043729590525E07125675
chr62957605929576215E07211297
chr62959015229590271E07225390
chr62959043729590525E07225675
chr62959749129597587E07232729
chr62957119529571304E0736433
chr62957181029571924E0737048
chr62957218729572252E0737425
chr62958034829580431E07315586
chr62958849729588657E07323735
chr62959015229590271E07325390
chr62959043729590525E07325675
chr62959086529590950E07326103
chr62959107629591182E07326314
chr62959168129592705E07326919
chr62959749129597587E07332729
chr62959812029598170E07333358
chr62959845629598506E07333694
chr62959865129598705E07333889
chr62960197229602095E07337210
chr62960215329602208E07337391
chr62960229629602597E07337534
chr62959107629591182E07426314
chr62957119529571304E0816433
chr62959749129597587E08132729
chr62959812029598170E08133358
chr62959845629598506E08133694
chr62959865129598705E08133889
chr62960215329602208E08137391
chr62960229629602597E08137534
chr62957181029571924E0827048
chr62957218729572252E0827425
chr62959168129592705E08226919










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr62952044329520803E067-43959
chr62952083029520919E067-43843
chr62952095229521847E067-42915
chr62959273229593051E06727970
chr62959320129593355E06728439
chr62959359529593846E06728833
chr62959400629594128E06729244
chr62959416329594272E06729401
chr62959438729594603E06729625
chr62959464829594713E06729886
chr62959475429595087E06729992
chr62959512529597042E06730363
chr62959971429601810E06734952
chr62959273229593051E06827970
chr62959320129593355E06828439
chr62959359529593846E06828833
chr62959400629594128E06829244
chr62959416329594272E06829401
chr62959438729594603E06829625
chr62959464829594713E06829886
chr62959475429595087E06829992
chr62959512529597042E06830363
chr62959971429601810E06834952
chr62952083029520919E069-43843
chr62959273229593051E06927970
chr62959320129593355E06928439
chr62959359529593846E06928833
chr62959400629594128E06929244
chr62959416329594272E06929401
chr62959438729594603E06929625
chr62959464829594713E06929886
chr62959475429595087E06929992
chr62959512529597042E06930363
chr62959971429601810E06934952
chr62959273229593051E07027970
chr62959320129593355E07028439
chr62959359529593846E07028833
chr62959400629594128E07029244
chr62959416329594272E07029401
chr62959438729594603E07029625
chr62959464829594713E07029886
chr62959475429595087E07029992
chr62959512529597042E07030363
chr62959971429601810E07034952
chr62952044329520803E071-43959
chr62952083029520919E071-43843
chr62959273229593051E07127970
chr62959320129593355E07128439
chr62959359529593846E07128833
chr62959400629594128E07129244
chr62959416329594272E07129401
chr62959438729594603E07129625
chr62959464829594713E07129886
chr62959475429595087E07129992
chr62959512529597042E07130363
chr62959971429601810E07134952
chr62952044329520803E072-43959
chr62952083029520919E072-43843
chr62952095229521847E072-42915
chr62959273229593051E07227970
chr62959320129593355E07228439
chr62959359529593846E07228833
chr62959400629594128E07229244
chr62959416329594272E07229401
chr62959438729594603E07229625
chr62959464829594713E07229886
chr62959475429595087E07229992
chr62959512529597042E07230363
chr62959971429601810E07234952
chr62952044329520803E073-43959
chr62952083029520919E073-43843
chr62959273229593051E07327970
chr62959320129593355E07328439
chr62959359529593846E07328833
chr62959400629594128E07329244
chr62959416329594272E07329401
chr62959438729594603E07329625
chr62959464829594713E07329886
chr62959475429595087E07329992
chr62959512529597042E07330363
chr62959971429601810E07334952
chr62952044329520803E074-43959
chr62952083029520919E074-43843
chr62959359529593846E07428833
chr62959400629594128E07429244
chr62959416329594272E07429401
chr62959438729594603E07429625
chr62959464829594713E07429886
chr62959475429595087E07429992
chr62959512529597042E07430363
chr62959971429601810E07434952
chr62959438729594603E08129625
chr62959464829594713E08129886
chr62959475429595087E08129992
chr62959971429601810E08134952
chr62952095229521847E082-42915
chr62959273229593051E08227970
chr62959320129593355E08228439
chr62959359529593846E08228833
chr62959400629594128E08229244
chr62959416329594272E08229401
chr62959438729594603E08229625
chr62959464829594713E08229886
chr62959475429595087E08229992
chr62959512529597042E08230363
chr62959971429601810E08234952