rs12988017

Homo sapiens
A>G
UGP2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0195 (5850/29872,GnomAD)
G=0138 (4021/29116,TOPMED)
G=0103 (517/5008,1000G)
G=0246 (947/3854,ALSPAC)
G=0252 (935/3708,TWINSUK)
chr2:63844466 (GRCh38.p7) (2p15)
AD
GWASdb2
1   publication(s)
See rs on genome
225 Enhancers around
48 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.63844466A>G
GRCh37.p13 chr 2NC_000002.11:g.64071600A>G

Gene: UGP2, UDP-glucose pyrophosphorylase 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
UGP2 transcript variant 2NM_001001521.1:c.N/AIntron Variant
UGP2 transcript variant 1NM_006759.3:c.N/AIntron Variant
UGP2 transcript variant X2XM_005264537.2:c.N/AIntron Variant
UGP2 transcript variant X1XM_005264538.1:c.N/AIntron Variant
UGP2 transcript variant X4XM_006712088.1:c.N/AIntron Variant
UGP2 transcript variant X12XM_011533091.1:c.N/AIntron Variant
UGP2 transcript variant X3XM_017004855.1:c.N/AIntron Variant
UGP2 transcript variant X6XM_017004856.1:c.N/AIntron Variant
UGP2 transcript variant X6XM_017004857.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.987G=0.013
1000GenomesAmericanSub694A=0.800G=0.200
1000GenomesEast AsianSub1008A=0.926G=0.074
1000GenomesEuropeSub1006A=0.787G=0.213
1000GenomesGlobalStudy-wide5008A=0.897G=0.103
1000GenomesSouth AsianSub978A=0.930G=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.754G=0.246
The Genome Aggregation DatabaseAfricanSub8704A=0.953G=0.047
The Genome Aggregation DatabaseAmericanSub838A=0.810G=0.190
The Genome Aggregation DatabaseEast AsianSub1620A=0.926G=0.074
The Genome Aggregation DatabaseEuropeSub18408A=0.721G=0.278
The Genome Aggregation DatabaseGlobalStudy-wide29872A=0.804G=0.195
The Genome Aggregation DatabaseOtherSub302A=0.880G=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29116A=0.861G=0.138
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.748G=0.252
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs129880170.00094alcohol dependence20201924

eQTL of rs12988017 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs12988017 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 )
chr26407228464072460E067684
chr26407247864072747E067878
chr26407289264073017E0671292
chr26407310864073328E0671508
chr26407634964077275E0674749
chr26407735764077407E0675757
chr26407785864078094E0676258
chr26407888564079168E0677285
chr26408016464080204E0678564
chr26408051664080702E0678916
chr26408072764080887E0679127
chr26408089664080975E0679296
chr26408101964081300E0679419
chr26408139964081580E0679799
chr26408162264081718E06710022
chr26408178664081902E06710186
chr26408191864081983E06710318
chr26408201464082140E06710414
chr26408219764082237E06710597
chr26409694264097025E06725342
chr26410154764101822E06729947
chr26410195164102964E06730351
chr26410300064103369E06731400
chr26411892364119039E06747323
chr26407228464072460E068684
chr26407247864072747E068878
chr26407289264073017E0681292
chr26407333364073517E0681733
chr26407356764073719E0681967
chr26407377364073861E0682173
chr26407458664074681E0682986
chr26407479264074879E0683192
chr26407494064075311E0683340
chr26407539664075455E0683796
chr26407578264076232E0684182
chr26407634964077275E0684749
chr26407735764077407E0685757
chr26407785864078094E0686258
chr26408051664080702E0688916
chr26408072764080887E0689127
chr26408089664080975E0689296
chr26408101964081300E0689419
chr26408139964081580E0689799
chr26408162264081718E06810022
chr26408178664081902E06810186
chr26408191864081983E06810318
chr26408201464082140E06810414
chr26408219764082237E06810597
chr26409694264097025E06825342
chr26409796164098068E06826361
chr26409829864098481E06826698
chr26409853164098599E06826931
chr26410154764101822E06829947
chr26410195164102964E06830351
chr26410300064103369E06831400
chr26410360664103732E06832006
chr26410377864104022E06832178
chr26410770964108197E06836109
chr26410839964108563E06836799
chr26411892364119039E06847323
chr26407228464072460E069684
chr26407247864072747E069878
chr26407289264073017E0691292
chr26407310864073328E0691508
chr26407333364073517E0691733
chr26407356764073719E0691967
chr26407377364073861E0692173
chr26407458664074681E0692986
chr26407735764077407E0695757
chr26407785864078094E0696258
chr26407921164079293E0697611
chr26408051664080702E0698916
chr26408072764080887E0699127
chr26408089664080975E0699296
chr26408101964081300E0699419
chr26408139964081580E0699799
chr26408162264081718E06910022
chr26408178664081902E06910186
chr26408191864081983E06910318
chr26408201464082140E06910414
chr26408219764082237E06910597
chr26410034964100399E06928749
chr26410154764101822E06929947
chr26410195164102964E06930351
chr26410300064103369E06931400
chr26407578264076232E0704182
chr26407634964077275E0704749
chr26404682864047331E071-24269
chr26404860764048692E071-22908
chr26406427264064600E071-7000
chr26407228464072460E071684
chr26407247864072747E071878
chr26407289264073017E0711292
chr26407310864073328E0711508
chr26407333364073517E0711733
chr26407356764073719E0711967
chr26407377364073861E0712173
chr26407458664074681E0712986
chr26407479264074879E0713192
chr26407494064075311E0713340
chr26407539664075455E0713796
chr26407578264076232E0714182
chr26407735764077407E0715757
chr26407888564079168E0717285
chr26407921164079293E0717611
chr26408101964081300E0719419
chr26408139964081580E0719799
chr26408162264081718E07110022
chr26408178664081902E07110186
chr26408191864081983E07110318
chr26408201464082140E07110414
chr26408219764082237E07110597
chr26408244264082520E07110842
chr26408256764082640E07110967
chr26408271364082901E07111113
chr26408292264082973E07111322
chr26408833764088701E07116737
chr26409796164098068E07126361
chr26409829864098481E07126698
chr26409853164098599E07126931
chr26409889764098988E07127297
chr26409918864099330E07127588
chr26410154764101822E07129947
chr26410195164102964E07130351
chr26410300064103369E07131400
chr26410360664103732E07132006
chr26410839964108563E07136799
chr26411571364115763E07144113
chr26411593364116246E07144333
chr26411892364119039E07147323
chr26406427264064600E072-7000
chr26407228464072460E072684
chr26407247864072747E072878
chr26407289264073017E0721292
chr26408051664080702E0728916
chr26408072764080887E0729127
chr26408089664080975E0729296
chr26408101964081300E0729419
chr26408139964081580E0729799
chr26408162264081718E07210022
chr26408178664081902E07210186
chr26408191864081983E07210318
chr26408201464082140E07210414
chr26408219764082237E07210597
chr26408244264082520E07210842
chr26408256764082640E07210967
chr26408271364082901E07211113
chr26408292264082973E07211322
chr26409694264097025E07225342
chr26409712964097179E07225529
chr26409796164098068E07226361
chr26410121164101303E07229611
chr26410154764101822E07229947
chr26410195164102964E07230351
chr26410300064103369E07231400
chr26411538864115469E07243788
chr26411571364115763E07244113
chr26411892364119039E07247323
chr26407228464072460E073684
chr26407247864072747E073878
chr26407289264073017E0731292
chr26407310864073328E0731508
chr26407333364073517E0731733
chr26407634964077275E0734749
chr26407921164079293E0737611
chr26408833764088701E07316737
chr26409997964100163E07328379
chr26410121164101303E07329611
chr26410154764101822E07329947
chr26410195164102964E07330351
chr26410300064103369E07331400
chr26411593364116246E07344333
chr26407228464072460E074684
chr26407247864072747E074878
chr26407289264073017E0741292
chr26407310864073328E0741508
chr26407333364073517E0741733
chr26407356764073719E0741967
chr26407377364073861E0742173
chr26407458664074681E0742986
chr26407479264074879E0743192
chr26407494064075311E0743340
chr26407539664075455E0743796
chr26407578264076232E0744182
chr26407634964077275E0744749
chr26407735764077407E0745757
chr26407785864078094E0746258
chr26407888564079168E0747285
chr26407921164079293E0747611
chr26408016464080204E0748564
chr26408051664080702E0748916
chr26408072764080887E0749127
chr26408089664080975E0749296
chr26408101964081300E0749419
chr26408139964081580E0749799
chr26408162264081718E07410022
chr26408178664081902E07410186
chr26408191864081983E07410318
chr26408201464082140E07410414
chr26408219764082237E07410597
chr26408244264082520E07410842
chr26408256764082640E07410967
chr26408271364082901E07411113
chr26408292264082973E07411322
chr26409694264097025E07425342
chr26409712964097179E07425529
chr26409997964100163E07428379
chr26410154764101822E07429947
chr26410195164102964E07430351
chr26410300064103369E07431400
chr26410360664103732E07432006
chr26410377864104022E07432178
chr26411571364115763E07444113
chr26411892364119039E07447323
chr26407634964077275E0814749
chr26410154764101822E08129947
chr26410195164102964E08130351
chr26410300064103369E08131400
chr26410360664103732E08132006
chr26410377864104022E08132178
chr26407634964077275E0824749
chr26407735764077407E0825757
chr26410154764101822E08229947
chr26410195164102964E08230351
chr26410300064103369E08231400










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr26406729064070236E067-1364
chr26407028364070351E067-1249
chr26407040664070537E067-1063
chr26407055564070609E067-991
chr26406729064070236E068-1364
chr26407028364070351E068-1249
chr26407040664070537E068-1063
chr26407055564070609E068-991
chr26406729064070236E069-1364
chr26407028364070351E069-1249
chr26407040664070537E069-1063
chr26407055564070609E069-991
chr26407066964070754E069-846
chr26407087964071000E069-600
chr26406729064070236E070-1364
chr26407028364070351E070-1249
chr26407040664070537E070-1063
chr26407055564070609E070-991
chr26407066964070754E070-846
chr26407087964071000E070-600
chr26406729064070236E071-1364
chr26407028364070351E071-1249
chr26407040664070537E071-1063
chr26407055564070609E071-991
chr26407066964070754E071-846
chr26406729064070236E072-1364
chr26407028364070351E072-1249
chr26407040664070537E072-1063
chr26407055564070609E072-991
chr26407066964070754E072-846
chr26406729064070236E073-1364
chr26407028364070351E073-1249
chr26407040664070537E073-1063
chr26407055564070609E073-991
chr26407066964070754E073-846
chr26406729064070236E074-1364
chr26407028364070351E074-1249
chr26407040664070537E074-1063
chr26407055564070609E074-991
chr26406729064070236E081-1364
chr26407028364070351E081-1249
chr26407040664070537E081-1063
chr26407055564070609E081-991
chr26406729064070236E082-1364
chr26407028364070351E082-1249
chr26407040664070537E082-1063
chr26407055564070609E082-991
chr26407066964070754E082-846