rs1476572

Homo sapiens
G>T
None
Check p-value
SNV (Single Nucleotide Variation)
G==0317 (9498/29900,GnomAD)
G==0293 (8557/29118,TOPMED)
G==0310 (1554/5008,1000G)
G==0283 (1092/3854,ALSPAC)
G==0278 (1030/3708,TWINSUK)
chr6:29706964 (GRCh38.p7) (6p22.1)
AD
GWASdb2
2   publication(s)
See rs on genome
41 Enhancers around
72 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.29706964G>T
GRCh37.p13 chr 6NC_000006.11:g.29674741G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.1193480T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.1193586T>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.972461T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.978057T>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.972506T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.978091T>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.1015999G>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.1015297G>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.972075T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.977695T>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.972325T>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.977910T>G

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.312T=0.688
1000GenomesAmericanSub694G=0.270T=0.730
1000GenomesEast AsianSub1008G=0.309T=0.691
1000GenomesEuropeSub1006G=0.304T=0.696
1000GenomesGlobalStudy-wide5008G=0.310T=0.690
1000GenomesSouth AsianSub978G=0.350T=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.283T=0.717
The Genome Aggregation DatabaseAfricanSub8708G=0.316T=0.684
The Genome Aggregation DatabaseAmericanSub838G=0.290T=0.710
The Genome Aggregation DatabaseEast AsianSub1604G=0.340T=0.660
The Genome Aggregation DatabaseEuropeSub18448G=0.317T=0.682
The Genome Aggregation DatabaseGlobalStudy-wide29900G=0.317T=0.682
The Genome Aggregation DatabaseOtherSub302G=0.300T=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.293T=0.706
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.278T=0.722
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
27766139Methodology for single nucleotide polymorphism selection in promoter regions for clinical use. An example of its applicability.Marques HInt J Mol Epidemiol Genet

P-Value

SNP ID p-value Traits Study
rs14765720.000589alcohol dependence20201924

eQTL of rs1476572 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:29674741RPL23AP1ENSG00000239257.1G>T3.1209e-7-19918Cerebellum
Chr6:29674741MICEENSG00000273340.1G>T7.2793e-10-38270Cerebellum
Chr6:29674741HLA-F-AS1ENSG00000214922.5G>T8.4756e-13-42029Cerebellum
Chr6:29674741HLA-HENSG00000206341.6G>T8.7137e-7-181503Cortex
Chr6:29674741MICEENSG00000273340.1G>T2.3222e-6-38270Cerebellar_Hemisphere
Chr6:29674741HLA-F-AS1ENSG00000214922.5G>T2.4717e-9-42029Cerebellar_Hemisphere
Chr6:29674741HLA-HENSG00000206341.6G>T2.5783e-22-181503Cerebellar_Hemisphere
Chr6:29674741HLA-HENSG00000206341.6G>T5.2793e-5-181503Caudate_basal_ganglia
Chr6:29674741HLA-KENSG00000230795.2G>T3.1711e-10-220214Hippocampus
Chr6:29674741HLA-KENSG00000230795.2G>T9.2361e-15-220214Nucleus_accumbens_basal_ganglia

meQTL of rs1476572 in Fetal Brain

Probe ID Position Gene beta p-value
cg22298860chr6:29690822HLA-F-0.07104277367772279.6047e-21
cg04186657chr6:29690893HLA-F-0.08220530931167311.5051e-13
cg11201654chr6:29690766HLA-F-0.08407446089837875.3821e-13
cg11768167chr6:29690889HLA-F-0.06891833114609111.7921e-12
cg21114334chr6:29720137IFITM4P-0.04765927628648322.9721e-9

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 )
chr62963028929630395E067-44346
chr62963047929630577E067-44164
chr62963362729634063E067-40678
chr62963415729634383E067-40358
chr62969271529692823E06717974
chr62963362729634063E068-40678
chr62963415729634383E068-40358
chr62969380329694252E06819062
chr62963123129631471E069-43270
chr62963148829631807E069-42934
chr62963362729634063E069-40678
chr62963415729634383E069-40358
chr62963446629635320E069-39421
chr62969311229693419E06918371
chr62963148829631807E071-42934
chr62963187729631934E071-42807
chr62963231529632365E071-42376
chr62963362729634063E071-40678
chr62963415729634383E071-40358
chr62963446629635320E071-39421
chr62967022329670696E071-4045
chr62969311229693419E07118371
chr62969344129693782E07118700
chr62969380329694252E07119062
chr62972139829721522E07146657
chr62963123129631471E072-43270
chr62963148829631807E072-42934
chr62963187729631934E072-42807
chr62963362729634063E072-40678
chr62963415729634383E072-40358
chr62963446629635320E072-39421
chr62968070729680766E0725966
chr62969271529692823E07217974
chr62969311229693419E07218371
chr62969271529692823E07317974
chr62969311229693419E07318371
chr62963338429633535E074-41206
chr62963362729634063E074-40678
chr62963415729634383E074-40358
chr62963446629635320E074-39421
chr62963547529635581E074-39160







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr62962499229625042E067-49699
chr62962600529626128E067-48613
chr62962768629627740E067-47001
chr62962935129629494E067-45247
chr62969068329691732E06715942
chr62969176029692347E06717019
chr62971613729717716E06741396
chr62971991229720033E06745171
chr62972005329720120E06745312
chr62972015629721181E06745415
chr62962499229625042E068-49699
chr62962600529626128E068-48613
chr62962768629627740E068-47001
chr62962935129629494E068-45247
chr62969068329691732E06815942
chr62969176029692347E06817019
chr62971613729717716E06841396
chr62971991229720033E06845171
chr62972005329720120E06845312
chr62972015629721181E06845415
chr62962499229625042E069-49699
chr62962600529626128E069-48613
chr62962768629627740E069-47001
chr62962935129629494E069-45247
chr62969068329691732E06915942
chr62969176029692347E06917019
chr62971613729717716E06941396
chr62971991229720033E06945171
chr62972005329720120E06945312
chr62972015629721181E06945415
chr62971991229720033E07045171
chr62972005329720120E07045312
chr62972015629721181E07045415
chr62962499229625042E071-49699
chr62962600529626128E071-48613
chr62962935129629494E071-45247
chr62969068329691732E07115942
chr62969176029692347E07117019
chr62971613729717716E07141396
chr62971991229720033E07145171
chr62972005329720120E07145312
chr62972015629721181E07145415
chr62962499229625042E072-49699
chr62962600529626128E072-48613
chr62962768629627740E072-47001
chr62969068329691732E07215942
chr62969176029692347E07217019
chr62971613729717716E07241396
chr62971991229720033E07245171
chr62972005329720120E07245312
chr62972015629721181E07245415
chr62962499229625042E073-49699
chr62962600529626128E073-48613
chr62962768629627740E073-47001
chr62969068329691732E07315942
chr62969176029692347E07317019
chr62971613729717716E07341396
chr62971991229720033E07345171
chr62972005329720120E07345312
chr62972015629721181E07345415
chr62962499229625042E074-49699
chr62962600529626128E074-48613
chr62962768629627740E074-47001
chr62962935129629494E074-45247
chr62969068329691732E07415942
chr62969176029692347E07417019
chr62971613729717716E07441396
chr62972015629721181E07445415
chr62969068329691732E08215942
chr62969176029692347E08217019
chr62971613729717716E08241396
chr62972015629721181E08245415