rs1610594

Homo sapiens
C>T
None
Check p-value
SNV (Single Nucleotide Variation)
C==0317 (9472/29874,GnomAD)
C==0293 (8550/29118,TOPMED)
C==0311 (1556/5008,1000G)
C==0283 (1092/3854,ALSPAC)
C==0279 (1034/3708,TWINSUK)
chr6:29711270 (GRCh38.p7) (6p22.1)
AD
GWASdb2
2   publication(s)
See rs on genome
41 Enhancers around
52 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.29711270C>T
GRCh37.p13 chr 6NC_000006.11:g.29679047C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.1197783T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.1197889T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.976755T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.982351T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.976800T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.982385T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.1020307C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.1019605C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.976369T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.981989T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.976615T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.982200T>C

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.312T=0.688
1000GenomesAmericanSub694C=0.270T=0.730
1000GenomesEast AsianSub1008C=0.309T=0.691
1000GenomesEuropeSub1006C=0.304T=0.696
1000GenomesGlobalStudy-wide5008C=0.311T=0.689
1000GenomesSouth AsianSub978C=0.350T=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.283T=0.717
The Genome Aggregation DatabaseAfricanSub8700C=0.316T=0.684
The Genome Aggregation DatabaseAmericanSub836C=0.280T=0.720
The Genome Aggregation DatabaseEast AsianSub1614C=0.338T=0.662
The Genome Aggregation DatabaseEuropeSub18422C=0.317T=0.682
The Genome Aggregation DatabaseGlobalStudy-wide29874C=0.317T=0.682
The Genome Aggregation DatabaseOtherSub302C=0.300T=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.293T=0.706
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.279T=0.721
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
rs16105940.000613alcohol dependence20201924

eQTL of rs1610594 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:29679047RPL23AP1ENSG00000239257.1C>T3.1209e-7-15612Cerebellum
Chr6:29679047MICEENSG00000273340.1C>T7.2793e-10-33964Cerebellum
Chr6:29679047HLA-F-AS1ENSG00000214922.5C>T8.4756e-13-37723Cerebellum
Chr6:29679047HLA-HENSG00000206341.6C>T8.7137e-7-177197Cortex
Chr6:29679047MICEENSG00000273340.1C>T2.3222e-6-33964Cerebellar_Hemisphere
Chr6:29679047HLA-F-AS1ENSG00000214922.5C>T2.4717e-9-37723Cerebellar_Hemisphere
Chr6:29679047HLA-HENSG00000206341.6C>T2.5783e-22-177197Cerebellar_Hemisphere
Chr6:29679047HLA-HENSG00000206341.6C>T5.2793e-5-177197Caudate_basal_ganglia
Chr6:29679047HLA-KENSG00000230795.2C>T3.1711e-10-215908Hippocampus
Chr6:29679047HLA-KENSG00000230795.2C>T9.2361e-15-215908Nucleus_accumbens_basal_ganglia

meQTL of rs1610594 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 )
chr62963028929630395E067-48652
chr62963047929630577E067-48470
chr62963362729634063E067-44984
chr62963415729634383E067-44664
chr62969271529692823E06713668
chr62963362729634063E068-44984
chr62963415729634383E068-44664
chr62969380329694252E06814756
chr62963123129631471E069-47576
chr62963148829631807E069-47240
chr62963362729634063E069-44984
chr62963415729634383E069-44664
chr62963446629635320E069-43727
chr62969311229693419E06914065
chr62963148829631807E071-47240
chr62963187729631934E071-47113
chr62963231529632365E071-46682
chr62963362729634063E071-44984
chr62963415729634383E071-44664
chr62963446629635320E071-43727
chr62967022329670696E071-8351
chr62969311229693419E07114065
chr62969344129693782E07114394
chr62969380329694252E07114756
chr62972139829721522E07142351
chr62963123129631471E072-47576
chr62963148829631807E072-47240
chr62963187729631934E072-47113
chr62963362729634063E072-44984
chr62963415729634383E072-44664
chr62963446629635320E072-43727
chr62968070729680766E0721660
chr62969271529692823E07213668
chr62969311229693419E07214065
chr62969271529692823E07313668
chr62969311229693419E07314065
chr62963338429633535E074-45512
chr62963362729634063E074-44984
chr62963415729634383E074-44664
chr62963446629635320E074-43727
chr62963547529635581E074-43466







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr62962935129629494E067-49553
chr62969068329691732E06711636
chr62969176029692347E06712713
chr62971613729717716E06737090
chr62971991229720033E06740865
chr62972005329720120E06741006
chr62972015629721181E06741109
chr62962935129629494E068-49553
chr62969068329691732E06811636
chr62969176029692347E06812713
chr62971613729717716E06837090
chr62971991229720033E06840865
chr62972005329720120E06841006
chr62972015629721181E06841109
chr62962935129629494E069-49553
chr62969068329691732E06911636
chr62969176029692347E06912713
chr62971613729717716E06937090
chr62971991229720033E06940865
chr62972005329720120E06941006
chr62972015629721181E06941109
chr62971991229720033E07040865
chr62972005329720120E07041006
chr62972015629721181E07041109
chr62962935129629494E071-49553
chr62969068329691732E07111636
chr62969176029692347E07112713
chr62971613729717716E07137090
chr62971991229720033E07140865
chr62972005329720120E07141006
chr62972015629721181E07141109
chr62969068329691732E07211636
chr62969176029692347E07212713
chr62971613729717716E07237090
chr62971991229720033E07240865
chr62972005329720120E07241006
chr62972015629721181E07241109
chr62969068329691732E07311636
chr62969176029692347E07312713
chr62971613729717716E07337090
chr62971991229720033E07340865
chr62972005329720120E07341006
chr62972015629721181E07341109
chr62962935129629494E074-49553
chr62969068329691732E07411636
chr62969176029692347E07412713
chr62971613729717716E07437090
chr62972015629721181E07441109
chr62969068329691732E08211636
chr62969176029692347E08212713
chr62971613729717716E08237090
chr62972015629721181E08241109