rs11647864

Homo sapiens
C>T
VPS4A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0057 (1713/29962,GnomAD)
T=0042 (1236/29118,TOPMED)
T=0029 (143/5008,1000G)
T=0072 (276/3854,ALSPAC)
T=0076 (280/3708,TWINSUK)
chr16:69321603 (GRCh38.p7) (16q22.1)
AD
GWASdb2
1   publication(s)
See rs on genome
211 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.69321603C>T
GRCh37.p13 chr 16NC_000016.9:g.69355506C>T

Gene: VPS4A, vacuolar protein sorting 4 homolog A(plus strand)

Molecule type Change Amino acid[Codon] SO Term
VPS4A transcriptNM_013245.2:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.996T=0.004
1000GenomesAmericanSub694C=0.960T=0.040
1000GenomesEast AsianSub1008C=0.978T=0.022
1000GenomesEuropeSub1006C=0.937T=0.063
1000GenomesGlobalStudy-wide5008C=0.971T=0.029
1000GenomesSouth AsianSub978C=0.980T=0.020
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.928T=0.072
The Genome Aggregation DatabaseAfricanSub8728C=0.986T=0.014
The Genome Aggregation DatabaseAmericanSub838C=0.960T=0.040
The Genome Aggregation DatabaseEast AsianSub1618C=0.983T=0.017
The Genome Aggregation DatabaseEuropeSub18476C=0.918T=0.081
The Genome Aggregation DatabaseGlobalStudy-wide29962C=0.942T=0.057
The Genome Aggregation DatabaseOtherSub302C=0.950T=0.050
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.957T=0.042
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.924T=0.076
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs116478640.000392alcohol dependence21314694

eQTL of rs11647864 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr16:69355506CIRH1AENSG00000141076.13C>T4.9558e-11190312Cerebellum
Chr16:69355506CIRH1AENSG00000141076.13C>T1.1634e-5190312Frontal_Cortex_BA9
Chr16:69355506CIRH1AENSG00000141076.13C>T6.1695e-13190312Cortex
Chr16:69355506CIRH1AENSG00000141076.13C>T7.1083e-6190312Cerebellar_Hemisphere
Chr16:69355506CIRH1AENSG00000141076.13C>T7.4588e-5190312Caudate_basal_ganglia
Chr16:69355506CIRH1AENSG00000141076.13C>T4.2715e-3190312Hippocampus
Chr16:69355506CIRH1AENSG00000141076.13C>T6.8235e-7190312Putamen_basal_ganglia
Chr16:69355506CIRH1AENSG00000141076.13C>T1.2007e-5190312Anterior_cingulate_cortex
Chr16:69355506CIRH1AENSG00000141076.13C>T5.0612e-5190312Nucleus_accumbens_basal_ganglia

meQTL of rs11647864 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 )
chr166934311069343665E067-11841
chr166934770269347752E067-7754
chr166934800069348050E067-7456
chr166934831669348446E067-7060
chr166934845869348770E067-6736
chr166934899469349044E067-6462
chr166934921069349250E067-6256
chr166934927469349334E067-6172
chr166934933669349386E067-6120
chr166934939469349438E067-6068
chr166934949469350776E067-4730
chr166935792669358006E0672420
chr166935813769358450E0672631
chr166935976369359859E0674257
chr166935998569360761E0674479
chr166936092669360980E0675420
chr166936225569362600E0676749
chr166937183269371882E06716326
chr166937194969372292E06716443
chr166937512869375217E06719622
chr166937536669375533E06719860
chr166937554469375584E06720038
chr166937739569377467E06721889
chr166937774469377798E06722238
chr166937821269378298E06722706
chr166937832569378403E06722819
chr166938987969389929E06734373
chr166938999269390042E06734486
chr166939025469390406E06734748
chr166934295769343070E068-12436
chr166934311069343665E068-11841
chr166934390769343957E068-11549
chr166934402869344200E068-11306
chr166935792669358006E0682420
chr166935813769358450E0682631
chr166935857569358793E0683069
chr166935880669358889E0683300
chr166935892869358988E0683422
chr166935998569360761E0684479
chr166936092669360980E0685420
chr166936100469361048E0685498
chr166936225569362600E0686749
chr166937140069371466E06815894
chr166937194969372292E06816443
chr166938987969389929E06834373
chr166938999269390042E06834486
chr166939008269390122E06834576
chr166939025469390406E06834748
chr166939056369390647E06835057
chr166939074569390964E06835239
chr166939099169391053E06835485
chr166939111869391168E06835612
chr166934311069343665E069-11841
chr166934759269347636E069-7870
chr166934770269347752E069-7754
chr166934800069348050E069-7456
chr166934831669348446E069-7060
chr166934845869348770E069-6736
chr166934899469349044E069-6462
chr166934921069349250E069-6256
chr166934927469349334E069-6172
chr166934933669349386E069-6120
chr166934939469349438E069-6068
chr166935976369359859E0694257
chr166935998569360761E0694479
chr166936092669360980E0695420
chr166936225569362600E0696749
chr166936788069368036E06912374
chr166937140069371466E06915894
chr166937160469371732E06916098
chr166937183269371882E06916326
chr166937194969372292E06916443
chr166937512869375217E06919622
chr166937536669375533E06919860
chr166937554469375584E06920038
chr166937574069375832E06920234
chr166938987969389929E06934373
chr166938999269390042E06934486
chr166939008269390122E06934576
chr166939025469390406E06934748
chr166939056369390647E06935057
chr166939074569390964E06935239
chr166939099169391053E06935485
chr166939111869391168E06935612
chr166934800069348050E070-7456
chr166935905469359237E0703548
chr166935968969359741E0704183
chr166935976369359859E0704257
chr166935998569360761E0704479
chr166936092669360980E0705420
chr166936100469361048E0705498
chr166936142769361494E0705921
chr166936193669361980E0706430
chr166936206969362129E0706563
chr166936225569362600E0706749
chr166937131069371360E07015804
chr166937140069371466E07015894
chr166937160469371732E07016098
chr166937183269371882E07016326
chr166937512869375217E07019622
chr166934311069343665E071-11841
chr166934713869347192E071-8314
chr166934759269347636E071-7870
chr166934770269347752E071-7754
chr166934800069348050E071-7456
chr166934831669348446E071-7060
chr166934845869348770E071-6736
chr166934899469349044E071-6462
chr166934921069349250E071-6256
chr166934927469349334E071-6172
chr166934933669349386E071-6120
chr166934939469349438E071-6068
chr166934949469350776E071-4730
chr166935792669358006E0712420
chr166935813769358450E0712631
chr166935857569358793E0713069
chr166935998569360761E0714479
chr166936225569362600E0716749
chr166937183269371882E07116326
chr166937194969372292E07116443
chr166937512869375217E07119622
chr166937536669375533E07119860
chr166937554469375584E07120038
chr166937739569377467E07121889
chr166937774469377798E07122238
chr166938987969389929E07134373
chr166938999269390042E07134486
chr166939008269390122E07134576
chr166939025469390406E07134748
chr166939056369390647E07135057
chr166939074569390964E07135239
chr166939099169391053E07135485
chr166939111869391168E07135612
chr166934311069343665E072-11841
chr166934831669348446E072-7060
chr166934845869348770E072-6736
chr166934899469349044E072-6462
chr166934921069349250E072-6256
chr166934927469349334E072-6172
chr166934933669349386E072-6120
chr166934939469349438E072-6068
chr166935792669358006E0722420
chr166935813769358450E0722631
chr166935976369359859E0724257
chr166935998569360761E0724479
chr166936092669360980E0725420
chr166936100469361048E0725498
chr166936142769361494E0725921
chr166936193669361980E0726430
chr166936206969362129E0726563
chr166936225569362600E0726749
chr166937194969372292E07216443
chr166938987969389929E07234373
chr166938999269390042E07234486
chr166939008269390122E07234576
chr166939025469390406E07234748
chr166939056369390647E07235057
chr166939074569390964E07235239
chr166939099169391053E07235485
chr166939111869391168E07235612
chr166931143169311775E073-43731
chr166934311069343665E073-11841
chr166934831669348446E073-7060
chr166934845869348770E073-6736
chr166935792669358006E0732420
chr166935813769358450E0732631
chr166935857569358793E0733069
chr166935880669358889E0733300
chr166935892869358988E0733422
chr166936092669360980E0735420
chr166936225569362600E0736749
chr166938987969389929E07334373
chr166938999269390042E07334486
chr166939008269390122E07334576
chr166939025469390406E07334748
chr166939056369390647E07335057
chr166939074569390964E07335239
chr166939099169391053E07335485
chr166939111869391168E07335612
chr166930942469309504E074-46002
chr166930951069309570E074-45936
chr166934295769343070E074-12436
chr166934311069343665E074-11841
chr166934831669348446E074-7060
chr166934845869348770E074-6736
chr166934899469349044E074-6462
chr166934921069349250E074-6256
chr166934927469349334E074-6172
chr166934933669349386E074-6120
chr166934939469349438E074-6068
chr166937554469375584E07420038
chr166937739569377467E07421889
chr166937774469377798E07422238
chr166937821269378298E07422706
chr166937832569378403E07422819
chr166938987969389929E07434373
chr166938999269390042E07434486
chr166939008269390122E07434576
chr166939025469390406E07434748
chr166935880669358889E0813300
chr166935892869358988E0813422
chr166936225569362600E0816749
chr166937160469371732E08116098
chr166937183269371882E08116326
chr166937194969372292E08116443
chr166935998569360761E0824479
chr166937131069371360E08215804
chr166937140069371466E08215894
chr166937160469371732E08216098
chr166937183269371882E08216326
chr166937194969372292E08216443










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr166934470369346489E067-9017
chr166936263969365329E0677133
chr166937282969374483E06717323
chr166934470369346489E068-9017
chr166936263969365329E0687133
chr166937282969374483E06817323
chr166934470369346489E069-9017
chr166936263969365329E0697133
chr166937282969374483E06917323
chr166934470369346489E070-9017
chr166936263969365329E0707133
chr166937282969374483E07017323
chr166934470369346489E071-9017
chr166936263969365329E0717133
chr166937282969374483E07117323
chr166934470369346489E072-9017
chr166936263969365329E0727133
chr166937282969374483E07217323
chr166934470369346489E073-9017
chr166936263969365329E0737133
chr166937282969374483E07317323
chr166934470369346489E074-9017
chr166936263969365329E0747133
chr166937282969374483E07417323
chr166934470369346489E081-9017
chr166937282969374483E08117323
chr166934470369346489E082-9017
chr166936263969365329E0827133
chr166937282969374483E08217323