rs429464

Homo sapiens
T>C
VAT1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0202 (6053/29930,GnomAD)
T==0200 (5830/29118,TOPMED)
T==0200 (1000/5008,1000G)
T==0180 (693/3854,ALSPAC)
T==0189 (699/3708,TWINSUK)
chr17:43018881 (GRCh38.p7) (17q21.31)
AD
GWASdb2
1   publication(s)
See rs on genome
202 Enhancers around
46 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 17NC_000017.11:g.43018881T>C
GRCh37.p13 chr 17NC_000017.10:g.41170898T>C

Gene: VAT1, vesicle amine transport 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
VAT1 transcriptNM_006373.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.249C=0.751
1000GenomesAmericanSub694T=0.180C=0.820
1000GenomesEast AsianSub1008T=0.081C=0.919
1000GenomesEuropeSub1006T=0.203C=0.797
1000GenomesGlobalStudy-wide5008T=0.200C=0.800
1000GenomesSouth AsianSub978T=0.260C=0.740
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.180C=0.820
The Genome Aggregation DatabaseAfricanSub8710T=0.221C=0.779
The Genome Aggregation DatabaseAmericanSub834T=0.130C=0.870
The Genome Aggregation DatabaseEast AsianSub1618T=0.077C=0.923
The Genome Aggregation DatabaseEuropeSub18466T=0.208C=0.791
The Genome Aggregation DatabaseGlobalStudy-wide29930T=0.202C=0.797
The Genome Aggregation DatabaseOtherSub302T=0.170C=0.830
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.200C=0.799
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.189C=0.811
PMID Title Author Journal
23953852Genome-wide association studies of maximum number of drinks.Pan YJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs4294642.45E-05alcohol consumption23953852

eQTL of rs429464 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Cerebellum
Chr17:41170898NBR1ENSG00000188554.9T>C5.5875e-15-151600Cerebellum
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Frontal_Cortex_BA9
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Hypothalamus
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Cortex
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Cerebellar_Hemisphere
Chr17:41170898NBR1ENSG00000188554.9T>C4.9078e-10-151600Cerebellar_Hemisphere
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Caudate_basal_ganglia
Chr17:41170898NBR2ENSG00000198496.6T>C4.0780e-25-106729Brain_Spinal_cord_cervical
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Hippocampus
Chr17:41170898NBR2ENSG00000198496.6T>C4.2072e-20-106729Substantia_nigra
Chr17:41170898NBR2ENSG00000198496.6T>C2.7000e-27-106729Putamen_basal_ganglia
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Anterior_cingulate_cortex
Chr17:41170898NBR2ENSG00000198496.6T>C0.0000e+0-106729Nucleus_accumbens_basal_ganglia
Chr17:41170898NBR2ENSG00000198496.6T>C4.6485e-22-106729Amygdala

meQTL of rs429464 in Fetal Brain

Probe ID Position Gene beta p-value
cg23758822chr17:414379820.1289973420152411.3459e-12

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 )
chr174115174641151797E067-19101
chr174115950141159612E067-11286
chr174118215941182246E06711261
chr174118225041182300E06711352
chr174118237241182504E06711474
chr174118606341186960E06715165
chr174118699741187203E06716099
chr174118797241188034E06717074
chr174113111741131371E068-39527
chr174113456941134645E068-36253
chr174113835141138503E068-32395
chr174114284941143008E068-27890
chr174114302141143178E068-27720
chr174115174641151797E068-19101
chr174116364341164250E068-6648
chr174116660641167197E068-3701
chr174116720841168256E068-2642
chr174116831441168440E068-2458
chr174116984041169970E068-928
chr174118143841181587E06810540
chr174118181141181918E06810913
chr174118194641182072E06811048
chr174118215941182246E06811261
chr174118225041182300E06811352
chr174118237241182504E06811474
chr174118574741185985E06814849
chr174118606341186960E06815165
chr174118699741187203E06816099
chr174118733241187384E06816434
chr174118756941187619E06816671
chr174118777141187839E06816873
chr174118797241188034E06817074
chr174118831541188637E06817417
chr174118867941188852E06817781
chr174113423841134288E069-36610
chr174113429841134355E069-36543
chr174113437941134516E069-36382
chr174113835141138503E069-32395
chr174113890541138951E069-31947
chr174115174641151797E069-19101
chr174117007141170259E069-639
chr174117027741171365E0690
chr174118194641182072E06911048
chr174118215941182246E06911261
chr174118225041182300E06911352
chr174118237241182504E06911474
chr174118606341186960E06915165
chr174118699741187203E06916099
chr174118733241187384E06916434
chr174118756941187619E06916671
chr174118777141187839E06916873
chr174118797241188034E06917074
chr174118831541188637E06917417
chr174118867941188852E06917781
chr174113111741131371E070-39527
chr174113409641134191E070-36707
chr174115180841152113E070-18785
chr174116502441165130E070-5768
chr174116517041165214E070-5684
chr174116525541165305E070-5593
chr174116530841165385E070-5513
chr174116547441165754E070-5144
chr174118080341180887E0709905
chr174118143841181587E07010540
chr174118574741185985E07014849
chr174118699741187203E07016099
chr174118733241187384E07016434
chr174118756941187619E07016671
chr174118777141187839E07016873
chr174118797241188034E07017074
chr174118831541188637E07017417
chr174119163141191681E07020733
chr174119179541191845E07020897
chr174119235941192579E07021461
chr174119267541192976E07021777
chr174119365541193730E07022757
chr174119384341194643E07022945
chr174119468941194755E07023791
chr174119484641194906E07023948
chr174113409641134191E071-36707
chr174113423841134288E071-36610
chr174113429841134355E071-36543
chr174113437941134516E071-36382
chr174115174641151797E071-19101
chr174115180841152113E071-18785
chr174115221541152294E071-18604
chr174115239841152455E071-18443
chr174117007141170259E071-639
chr174117027741171365E0710
chr174117142041172669E071522
chr174118194641182072E07111048
chr174118215941182246E07111261
chr174118225041182300E07111352
chr174118237241182504E07111474
chr174118606341186960E07115165
chr174118699741187203E07116099
chr174118733241187384E07116434
chr174118756941187619E07116671
chr174118777141187839E07116873
chr174118797241188034E07117074
chr174118867941188852E07117781
chr174113111741131371E072-39527
chr174113409641134191E072-36707
chr174113423841134288E072-36610
chr174113429841134355E072-36543
chr174113437941134516E072-36382
chr174113456941134645E072-36253
chr174115174641151797E072-19101
chr174116720841168256E072-2642
chr174116831441168440E072-2458
chr174116847241168645E072-2253
chr174116866441168744E072-2154
chr174117007141170259E072-639
chr174117027741171365E0720
chr174117142041172669E072522
chr174118194641182072E07211048
chr174118215941182246E07211261
chr174118225041182300E07211352
chr174118237241182504E07211474
chr174118606341186960E07215165
chr174118699741187203E07216099
chr174118733241187384E07216434
chr174118756941187619E07216671
chr174118777141187839E07216873
chr174118797241188034E07217074
chr174118831541188637E07217417
chr174113409641134191E073-36707
chr174113423841134288E073-36610
chr174113429841134355E073-36543
chr174113437941134516E073-36382
chr174113456941134645E073-36253
chr174115180841152113E073-18785
chr174116660641167197E073-3701
chr174116720841168256E073-2642
chr174116831441168440E073-2458
chr174116847241168645E073-2253
chr174116984041169970E073-928
chr174117007141170259E073-639
chr174117027741171365E0730
chr174118215941182246E07311261
chr174118225041182300E07311352
chr174118237241182504E07311474
chr174118606341186960E07315165
chr174118699741187203E07316099
chr174118797241188034E07317074
chr174115174641151797E074-19101
chr174115180841152113E074-18785
chr174116547441165754E074-5144
chr174116577241165867E074-5031
chr174116588441165987E074-4911
chr174116603041166568E074-4330
chr174116831441168440E074-2458
chr174117007141170259E074-639
chr174117027741171365E0740
chr174117142041172669E074522
chr174118143841181587E07410540
chr174118181141181918E07410913
chr174118194641182072E07411048
chr174118215941182246E07411261
chr174118225041182300E07411352
chr174118237241182504E07411474
chr174118606341186960E07415165
chr174118699741187203E07416099
chr174118733241187384E07416434
chr174118756941187619E07416671
chr174118777141187839E07416873
chr174118797241188034E07417074
chr174118831541188637E07417417
chr174118867941188852E07417781
chr174113409641134191E081-36707
chr174113423841134288E081-36610
chr174113429841134355E081-36543
chr174113437941134516E081-36382
chr174115180841152113E081-18785
chr174117007141170259E081-639
chr174117027741171365E0810
chr174117142041172669E081522
chr174118048041180793E0819582
chr174118080341180887E0819905
chr174118143841181587E08110540
chr174118606341186960E08115165
chr174118699741187203E08116099
chr174118733241187384E08116434
chr174118756941187619E08116671
chr174118777141187839E08116873
chr174118797241188034E08117074
chr174118831541188637E08117417
chr174119365541193730E08122757
chr174119384341194643E08122945
chr174113409641134191E082-36707
chr174113423841134288E082-36610
chr174113429841134355E082-36543
chr174113437941134516E082-36382
chr174117007141170259E082-639
chr174117027741171365E0820
chr174118541941185632E08214521
chr174118564041185696E08214742
chr174118574741185985E08214849
chr174118606341186960E08215165
chr174118831541188637E08217417
chr174118867941188852E08217781
chr174119384341194643E08222945










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr174113137441133767E067-37131
chr174114895241151189E067-19709
chr174115848841159341E067-11557
chr174117293441174642E0672036
chr174117632741178417E0675429
chr174113137441133767E068-37131
chr174114895241151189E068-19709
chr174115848841159341E068-11557
chr174117293441174642E0682036
chr174117632741178417E0685429
chr174113137441133767E069-37131
chr174114895241151189E069-19709
chr174115848841159341E069-11557
chr174117293441174642E0692036
chr174117632741178417E0695429
chr174113137441133767E070-37131
chr174114895241151189E070-19709
chr174117293441174642E0702036
chr174117632741178417E0705429
chr174113137441133767E071-37131
chr174114895241151189E071-19709
chr174115848841159341E071-11557
chr174117293441174642E0712036
chr174117632741178417E0715429
chr174113137441133767E072-37131
chr174114895241151189E072-19709
chr174115848841159341E072-11557
chr174117293441174642E0722036
chr174117632741178417E0725429
chr174113137441133767E073-37131
chr174114895241151189E073-19709
chr174115848841159341E073-11557
chr174117293441174642E0732036
chr174117632741178417E0735429
chr174113137441133767E074-37131
chr174114895241151189E074-19709
chr174115848841159341E074-11557
chr174117293441174642E0742036
chr174117632741178417E0745429
chr174113137441133767E081-37131
chr174114895241151189E081-19709
chr174117293441174642E0812036
chr174113137441133767E082-37131
chr174114895241151189E082-19709
chr174117293441174642E0822036
chr174117632741178417E0825429