rs2857103

Homo sapiens
C>A
TAP2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0366 (10679/29118,TOPMED)
A=0361 (10315/28504,GnomAD)
A=0399 (1998/5008,1000G)
A=0288 (1109/3854,ALSPAC)
A=0279 (1035/3708,TWINSUK)
chr6:32823522 (GRCh38.p7) (6p21.32)
AD
GWASdb2
2   publication(s)
See rs on genome
18 Enhancers around
35 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.32823522C>A
GRCh37.p13 chr 6NC_000006.11:g.32791299C>A
TAP2 RefSeqGeneNG_009793.3:g.20249G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.4235722C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.4235828C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.4122608C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.4128193C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.4017809C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.4023405C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.4067238A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.4072823A>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.4222925A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.4222223A>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.4242874C>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.4248494C>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.2:g.4128537A>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1NT_167244.1:g.4078453A>C

Gene: TAP2, transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)(minus strand)

Molecule type Change Amino acid[Codon] SO Term
TAP2 transcript variant 2NM_018833.2:c.N/AIntron Variant
TAP2 transcript variant 1, B alleleNM_000544.3:c.N/AGenic Downstream Transcript Variant
TAP2 transcript variant 1, A alleleNM_001290043.1:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.599A=0.401
1000GenomesAmericanSub694C=0.610A=0.390
1000GenomesEast AsianSub1008C=0.603A=0.397
1000GenomesEuropeSub1006C=0.657A=0.343
1000GenomesGlobalStudy-wide5008C=0.601A=0.399
1000GenomesSouth AsianSub978C=0.540A=0.460
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.712A=0.288
The Genome Aggregation DatabaseAfricanSub8384C=0.625A=0.375
The Genome Aggregation DatabaseAmericanSub780C=0.560A=0.440
The Genome Aggregation DatabaseEast AsianSub1598C=0.613A=0.387
The Genome Aggregation DatabaseEuropeSub17442C=0.650A=0.349
The Genome Aggregation DatabaseGlobalStudy-wide28504C=0.638A=0.361
The Genome Aggregation DatabaseOtherSub300C=0.580A=0.420
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.633A=0.366
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.721A=0.279
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
27325005Association of polymorphisms of the transporter associated with antigen processing (TAP2) gene with pulmonary tuberculosis in an elderly Japanese population.Thu KSAPMIS

P-Value

SNP ID p-value Traits Study
rs28571030.00083alcohol dependence20201924

eQTL of rs2857103 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.9928e-146474Cerebellum
Chr6:32791299HLA-DOBENSG00000241106.2C>A4.7721e-116474Frontal_Cortex_BA9
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.1851e-86474Hypothalamus
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.0541e-136474Cortex
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.6154e-96474Cerebellar_Hemisphere
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.9928e-116474Caudate_basal_ganglia
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.8342e-46474Brain_Spinal_cord_cervical
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.0737e-76474Hippocampus
Chr6:32791299HLA-DOBENSG00000241106.2C>A1.4959e-46474Substantia_nigra
Chr6:32791299HLA-DOBENSG00000241106.2C>A6.9503e-96474Putamen_basal_ganglia
Chr6:32791299HLA-DOBENSG00000241106.2C>A5.3216e-66474Anterior_cingulate_cortex
Chr6:32791299HLA-DOBENSG00000241106.2C>A2.6012e-106474Nucleus_accumbens_basal_ganglia
Chr6:32791299HLA-DOBENSG00000241106.2C>A4.9962e-46474Amygdala

meQTL of rs2857103 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 )
chr63279376932794052E0672470
chr63280471032804798E06713411
chr63281382432813885E06822525
chr63281388832814070E06822589
chr63281974032819875E06828441
chr63281974032819875E06928441
chr63279376932794052E0712470
chr63279425732794358E0712958
chr63281974032819875E07128441
chr63279376932794052E0722470
chr63279425732794358E0722958
chr63281974032819875E07228441
chr63279425732794358E0732958
chr63280471032804798E07313411
chr63281974032819875E07328441
chr63281053632810768E07419237
chr63281974032819875E07428441
chr63283579032836343E07444491







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr63280573732806948E06714438
chr63281103432813766E06719735
chr63282033232820414E06729033
chr63282043532822762E06729136
chr63280573732806948E06814438
chr63281103432813766E06819735
chr63282033232820414E06829033
chr63282043532822762E06829136
chr63280573732806948E06914438
chr63281103432813766E06919735
chr63282033232820414E06929033
chr63282043532822762E06929136
chr63280573732806948E07014438
chr63281103432813766E07019735
chr63282033232820414E07029033
chr63282043532822762E07029136
chr63280573732806948E07114438
chr63281103432813766E07119735
chr63282033232820414E07129033
chr63282043532822762E07129136
chr63280573732806948E07214438
chr63281103432813766E07219735
chr63282033232820414E07229033
chr63282043532822762E07229136
chr63280573732806948E07314438
chr63281103432813766E07319735
chr63282033232820414E07329033
chr63282043532822762E07329136
chr63280573732806948E07414438
chr63281103432813766E07419735
chr63282033232820414E07429033
chr63282043532822762E07429136
chr63280573732806948E08214438
chr63281103432813766E08219735
chr63282043532822762E08229136