rs7930569

Homo sapiens
A>G
PDDC1 : Synonymous Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0482 (55986/116152,ExAC)
G=0462 (13816/29884,GnomAD)
G=0433 (12630/29118,TOPMED)
A==0440 (5734/13004,GO-ESP)
G=0433 (2166/5008,1000G)
G=0490 (1889/3854,ALSPAC)
G=0485 (1797/3708,TWINSUK)
chr11:771034 (GRCh38.p7) (11p15.5)
AD
GWASdb2
1   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.771034A>G
GRCh37.p13 chr 11NC_000011.9:g.771034A>G

Gene: PDDC1, Parkinson disease 7 domain containing 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
GATD1 transcript variant 2NM_001318818.1:c....NM_001318818.1:c.465T>CT [ACT]> T [ACC]Coding Sequence Variant
glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 2NP_001305747.1:p....NP_001305747.1:p.Thr155=T [Thr]> T [Thr]Synonymous Variant
GATD1 transcript variant 1NM_182612.3:c.615T>CT [ACT]> T [ACC]Coding Sequence Variant
glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 1 precursorNP_872418.1:p.Thr...NP_872418.1:p.Thr205=T [Thr]> T [Thr]Synonymous Variant
GATD1 transcript variant 4NM_001318821.1:c....NM_001318821.1:c.615T>CT [ACT]> T [ACC]Coding Sequence Variant
glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 4 precursorNP_001305750.1:p....NP_001305750.1:p.Thr205=T [Thr]> T [Thr]Synonymous Variant
GATD1 transcript variant 5NM_001318822.1:c....NM_001318822.1:c.357T>CT [ACT]> T [ACC]Coding Sequence Variant
glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 5NP_001305751.1:p....NP_001305751.1:p.Thr119=T [Thr]> T [Thr]Synonymous Variant
GATD1 transcript variant 7NM_001318824.1:c....NM_001318824.1:c.507T>CT [ACT]> T [ACC]Coding Sequence Variant
glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 7NP_001305753.1:p....NP_001305753.1:p.Thr169=T [Thr]> T [Thr]Synonymous Variant
GATD1 transcript variant 6NM_001318823.1:c....NM_001318823.1:c.465T>CT [ACT]> T [ACC]Coding Sequence Variant
glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 6NP_001305752.1:p....NP_001305752.1:p.Thr155=T [Thr]> T [Thr]Synonymous Variant
GATD1 transcript variant 3NM_001318820.1:c....NM_001318820.1:c.507T>CT [ACT]> T [ACC]Coding Sequence Variant
glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 3NP_001305749.1:p....NP_001305749.1:p.Thr169=T [Thr]> T [Thr]Synonymous Variant
GATD1 transcript variant 9NR_134868.1:n.749T>CT>CNon Coding Transcript Variant
GATD1 transcript variant 8NR_134867.1:n.686T>CT>CNon Coding Transcript Variant
PDDC1 transcript variant X2XM_017017661.1:c.N/AIntron Variant
PDDC1 transcript variant X9XM_017017665.1:c.N/AIntron Variant
GATD1 transcript variant X5XM_017017664.1:c.N/A3 Prime UTR Variant
GATD1 transcript variant X8XM_017017667.1:c.N/A3 Prime UTR Variant
GATD1 transcript variant X10XM_017017668.1:c.N/A3 Prime UTR Variant
GATD1 transcript variant X6XM_005252898.2:c.N/AGenic Downstream Transcript Variant
PDDC1 transcript variant X5XM_011520064.1:c.N/AGenic Downstream Transcript Variant
GATD1 transcript variant X2XM_017017662.1:c.N/AGenic Downstream Transcript Variant
PDDC1 transcript variant X1XM_017017660.1:c....XM_017017660.1:c.615T>CT [ACT]> T [ACC]Coding Sequence Variant
Parkinson disease 7 domain-containing protein 1 isoform X1XP_016873149.1:p....XP_016873149.1:p.Thr205=T [Thr]> T [Thr]Synonymous Variant
PDDC1 transcript variant X4XM_017017663.1:c....XM_017017663.1:c.507T>CT [ACT]> T [ACC]Coding Sequence Variant
Parkinson disease 7 domain-containing protein 1 isoform X4XP_016873152.1:p....XP_016873152.1:p.Thr169=T [Thr]> T [Thr]Synonymous Variant
PDDC1 transcript variant X10XM_017017666.1:c....XM_017017666.1:c.465T>CT [ACT]> T [ACC]Coding Sequence Variant
Parkinson disease 7 domain-containing protein 1 isoform X7XP_016873155.1:p....XP_016873155.1:p.Thr155=T [Thr]> T [Thr]Synonymous Variant
PDDC1 transcript variant X7XR_001747859.1:n....XR_001747859.1:n.681T>CT>CNon Coding Transcript Variant
GATD1 transcript variant X9XR_242802.3:n.815T>CT>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.694G=0.306
1000GenomesAmericanSub694A=0.400G=0.600
1000GenomesEast AsianSub1008A=0.439G=0.561
1000GenomesEuropeSub1006A=0.557G=0.443
1000GenomesGlobalStudy-wide5008A=0.567G=0.433
1000GenomesSouth AsianSub978A=0.660G=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.510G=0.490
The Exome Aggregation ConsortiumAmericanSub20932A=0.502G=0.497
The Exome Aggregation ConsortiumAsianSub24516A=0.569G=0.430
The Exome Aggregation ConsortiumEuropeSub69852A=0.504G=0.495
The Exome Aggregation ConsortiumGlobalStudy-wide116152A=0.517G=0.482
The Exome Aggregation ConsortiumOtherSub852A=0.560G=0.440
The Genome Aggregation DatabaseAfricanSub8712A=0.669G=0.331
The Genome Aggregation DatabaseAmericanSub836A=0.410G=0.590
The Genome Aggregation DatabaseEast AsianSub1610A=0.444G=0.556
The Genome Aggregation DatabaseEuropeSub18424A=0.488G=0.511
The Genome Aggregation DatabaseGlobalStudy-wide29884A=0.537G=0.462
The Genome Aggregation DatabaseOtherSub302A=0.580G=0.420
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.566G=0.433
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.515G=0.485
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
rs79305690.000692alcohol dependence20201924

eQTL of rs7930569 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr11:771034AP006621.5ENSG00000255284.1A>G0.0000e+0-6544Cerebellum
Chr11:771034AP006621.1ENSG00000177236.3A>G0.0000e+0-9083Cerebellum
Chr11:771034AP006621.6ENSG00000255142.1A>G5.6352e-14-10611Cerebellum
Chr11:771034PIDDENSG00000177595.13A>G3.4501e-24-38612Cerebellum
Chr11:771034AP006621.5ENSG00000255284.1A>G5.6214e-9-6544Frontal_Cortex_BA9
Chr11:771034AP006621.1ENSG00000177236.3A>G1.0231e-24-9083Frontal_Cortex_BA9
Chr11:771034AP006621.5ENSG00000255284.1A>G3.2067e-8-6544Hypothalamus
Chr11:771034AP006621.1ENSG00000177236.3A>G1.1796e-23-9083Hypothalamus
Chr11:771034AP006621.5ENSG00000255284.1A>G2.3594e-22-6544Cortex
Chr11:771034AP006621.1ENSG00000177236.3A>G0.0000e+0-9083Cortex
Chr11:771034AP006621.6ENSG00000255142.1A>G1.3855e-7-10611Cortex
Chr11:771034PNPLA2ENSG00000177666.11A>G9.1741e-19-47868Cortex
Chr11:771034AP006621.5ENSG00000255284.1A>G1.5753e-18-6544Cerebellar_Hemisphere
Chr11:771034AP006621.1ENSG00000177236.3A>G0.0000e+0-9083Cerebellar_Hemisphere
Chr11:771034AP006621.6ENSG00000255142.1A>G2.9412e-9-10611Cerebellar_Hemisphere
Chr11:771034PIDDENSG00000177595.13A>G1.5931e-19-38612Cerebellar_Hemisphere
Chr11:771034AP006621.5ENSG00000255284.1A>G4.1271e-15-6544Caudate_basal_ganglia
Chr11:771034AP006621.1ENSG00000177236.3A>G0.0000e+0-9083Caudate_basal_ganglia
Chr11:771034AP006621.6ENSG00000255142.1A>G1.1145e-6-10611Caudate_basal_ganglia
Chr11:771034AP006621.5ENSG00000255284.1A>G1.4912e-5-6544Brain_Spinal_cord_cervical
Chr11:771034AP006621.1ENSG00000177236.3A>G3.2592e-18-9083Brain_Spinal_cord_cervical
Chr11:771034AP006621.5ENSG00000255284.1A>G1.5303e-9-6544Hippocampus
Chr11:771034AP006621.1ENSG00000177236.3A>G1.6000e-27-9083Hippocampus
Chr11:771034AP006621.1ENSG00000177236.3A>G7.2880e-12-9083Substantia_nigra
Chr11:771034AP006621.5ENSG00000255284.1A>G2.7268e-11-6544Putamen_basal_ganglia
Chr11:771034AP006621.1ENSG00000177236.3A>G3.8386e-24-9083Putamen_basal_ganglia
Chr11:771034AP006621.5ENSG00000255284.1A>G2.9482e-6-6544Anterior_cingulate_cortex
Chr11:771034AP006621.1ENSG00000177236.3A>G0.0000e+0-9083Anterior_cingulate_cortex
Chr11:771034AP006621.5ENSG00000255284.1A>G8.5577e-16-6544Nucleus_accumbens_basal_ganglia
Chr11:771034AP006621.1ENSG00000177236.3A>G3.0000e-28-9083Nucleus_accumbens_basal_ganglia
Chr11:771034AP006621.6ENSG00000255142.1A>G2.2382e-7-10611Nucleus_accumbens_basal_ganglia
Chr11:771034AP006621.5ENSG00000255284.1A>G5.5118e-7-6544Amygdala
Chr11:771034AP006621.1ENSG00000177236.3A>G2.7881e-17-9083Amygdala

meQTL of rs7930569 in Fetal Brain

Probe ID Position Gene beta p-value
cg17628894chr11:804452LRDD-0.0270349950847391.8413e-10
cg13353733chr11:773106PDDC1-0.03762266573906452.1422e-9
cg01741372chr11:7838890.03431619925608222.6904e-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 )
chr11727417728717E067-42317
chr11728753728835E067-42199
chr11728925728978E067-42056
chr11728992729078E067-41956
chr11729142729221E067-41813
chr11737389738334E067-32700
chr11738365738488E067-32546
chr11749299749351E067-21683
chr11749452749506E067-21528
chr11750200750250E067-20784
chr11752476752526E067-18508
chr11752652752702E067-18332
chr11752783752898E067-18136
chr11761685761879E067-9155
chr11761975762015E067-9019
chr11762139762189E067-8845
chr11762288763622E067-7412
chr11771415771535E067381
chr11771654771708E067620
chr11771767771897E067733
chr11771964772195E067930
chr11772467772517E0671433
chr11772966773229E0671932
chr11773359773423E0672325
chr11773474773524E0672440
chr11773660773790E0672626
chr11773804774001E0672770
chr11774037774168E0673003
chr11783370784241E06712336
chr11811429812418E06740395
chr11727300727406E068-43628
chr11727417728717E068-42317
chr11728753728835E068-42199
chr11728925728978E068-42056
chr11728992729078E068-41956
chr11729142729221E068-41813
chr11729296730085E068-40949
chr11730127730190E068-40844
chr11738365738488E068-32546
chr11749299749351E068-21683
chr11749452749506E068-21528
chr11749789749876E068-21158
chr11749926750044E068-20990
chr11750200750250E068-20784
chr11762288763622E068-7412
chr11771654771708E068620
chr11771767771897E068733
chr11771964772195E068930
chr11772467772517E0681433
chr11772664772728E0681630
chr11772833772924E0681799
chr11773804774001E0682770
chr11774037774168E0683003
chr11775008775954E0683974
chr11782822783126E06811788
chr11783166783235E06812132
chr11783370784241E06812336
chr11794043794710E06823009
chr11727417728717E069-42317
chr11730127730190E069-40844
chr11736533736770E069-34264
chr11737157737221E069-33813
chr11737243737305E069-33729
chr11737389738334E069-32700
chr11749299749351E069-21683
chr11749452749506E069-21528
chr11749789749876E069-21158
chr11749926750044E069-20990
chr11761685761879E069-9155
chr11761975762015E069-9019
chr11762139762189E069-8845
chr11762288763622E069-7412
chr11763800764270E069-6764
chr11764277764571E069-6463
chr11764687764950E069-6084
chr11764999765081E069-5953
chr11765118765640E069-5394
chr11771654771708E069620
chr11771767771897E069733
chr11771964772195E069930
chr11772467772517E0691433
chr11772664772728E0691630
chr11772833772924E0691799
chr11772966773229E0691932
chr11773359773423E0692325
chr11773474773524E0692440
chr11773660773790E0692626
chr11773804774001E0692770
chr11774037774168E0693003
chr11774412774546E0693378
chr11775008775954E0693974
chr11778786778866E0697752
chr11782822783126E06911788
chr11783166783235E06912132
chr11783370784241E06912336
chr11811429812418E06940395
chr11725421727287E070-43747
chr11772467772517E0701433
chr11772664772728E0701630
chr11772833772924E0701799
chr11772966773229E0701932
chr11773359773423E0702325
chr11773474773524E0702440
chr11773660773790E0702626
chr11773804774001E0702770
chr11774037774168E0703003
chr11774412774546E0703378
chr11775008775954E0703974
chr11778786778866E0707752
chr11778878778990E0707844
chr11779041779261E0708007
chr11783370784241E07012336
chr11793350794013E07022316
chr11794043794710E07023009
chr11802799803038E07031765
chr11803170803233E07032136
chr11803237803529E07032203
chr11803550803788E07032516
chr11725421727287E071-43747
chr11742180742581E071-28453
chr11742595742669E071-28365
chr11742894742944E071-28090
chr11742963743081E071-27953
chr11746015746155E071-24879
chr11749299749351E071-21683
chr11749452749506E071-21528
chr11749789749876E071-21158
chr11749926750044E071-20990
chr11762288763622E071-7412
chr11763688763754E071-7280
chr11763800764270E071-6764
chr11764277764571E071-6463
chr11764687764950E071-6084
chr11764999765081E071-5953
chr11765118765640E071-5394
chr11770525770608E071-426
chr11770624770725E071-309
chr11771050771259E07116
chr11771415771535E071381
chr11771654771708E071620
chr11771767771897E071733
chr11771964772195E071930
chr11772467772517E0711433
chr11773660773790E0712626
chr11773804774001E0712770
chr11774037774168E0713003
chr11775008775954E0713974
chr11783370784241E07112336
chr11794043794710E07123009
chr11811429812418E07140395
chr11812431812503E07141397
chr11812514812747E07141480
chr11722670722758E072-48276
chr11723105723720E072-47314
chr11727417728717E072-42317
chr11728753728835E072-42199
chr11728925728978E072-42056
chr11728992729078E072-41956
chr11736533736770E072-34264
chr11737157737221E072-33813
chr11737243737305E072-33729
chr11737389738334E072-32700
chr11749299749351E072-21683
chr11749452749506E072-21528
chr11749789749876E072-21158
chr11749926750044E072-20990
chr11761685761879E072-9155
chr11761975762015E072-9019
chr11762139762189E072-8845
chr11762288763622E072-7412
chr11765118765640E072-5394
chr11771654771708E072620
chr11771767771897E072733
chr11771964772195E072930
chr11772467772517E0721433
chr11773474773524E0722440
chr11773660773790E0722626
chr11775008775954E0723974
chr11782822783126E07211788
chr11783166783235E07212132
chr11783370784241E07212336
chr11793350794013E07222316
chr11727417728717E073-42317
chr11728753728835E073-42199
chr11728925728978E073-42056
chr11728992729078E073-41956
chr11730127730190E073-40844
chr11749299749351E073-21683
chr11749452749506E073-21528
chr11749789749876E073-21158
chr11749926750044E073-20990
chr11752476752526E073-18508
chr11752652752702E073-18332
chr11752783752898E073-18136
chr11761975762015E073-9019
chr11762139762189E073-8845
chr11762288763622E073-7412
chr11771654771708E073620
chr11771767771897E073733
chr11771964772195E073930
chr11772467772517E0731433
chr11772664772728E0731630
chr11772833772924E0731799
chr11775008775954E0733974
chr11778786778866E0737752
chr11778878778990E0737844
chr11779041779261E0738007
chr11779293779616E0738259
chr11779619779776E0738585
chr11779811779900E0738777
chr11779930780125E0738896
chr11780217780315E0739183
chr11780321780361E0739287
chr11780399780492E0739365
chr11783370784241E07312336
chr11785044785136E07314010
chr11785293785337E07314259
chr11785954786034E07314920
chr11786105786190E07315071
chr11786217786267E07315183
chr11786324786378E07315290
chr11786409786611E07315375
chr11786661786712E07315627
chr11786833786984E07315799
chr11787055787175E07316021
chr11787180787380E07316146
chr11787407787592E07316373
chr11787641787729E07316607
chr11787747787803E07316713
chr11787852787935E07316818
chr11787986788159E07316952
chr11788166788267E07317132
chr11788283788451E07317249
chr11788544788603E07317510
chr11788685788733E07317651
chr11788757788839E07317723
chr11793350794013E07322316
chr11798811798876E07327777
chr11798996799393E07327962
chr11803550803788E07332516
chr11811429812418E07340395
chr11727417728717E074-42317
chr11728753728835E074-42199
chr11728925728978E074-42056
chr11728992729078E074-41956
chr11729142729221E074-41813
chr11736533736770E074-34264
chr11737157737221E074-33813
chr11737243737305E074-33729
chr11737389738334E074-32700
chr11742180742581E074-28453
chr11742595742669E074-28365
chr11749299749351E074-21683
chr11749452749506E074-21528
chr11752476752526E074-18508
chr11752652752702E074-18332
chr11752783752898E074-18136
chr11761685761879E074-9155
chr11761975762015E074-9019
chr11762139762189E074-8845
chr11762288763622E074-7412
chr11764999765081E074-5953
chr11765118765640E074-5394
chr11771654771708E074620
chr11771767771897E074733
chr11771964772195E074930
chr11772467772517E0741433
chr11772664772728E0741630
chr11772966773229E0741932
chr11773359773423E0742325
chr11773474773524E0742440
chr11773660773790E0742626
chr11773804774001E0742770
chr11774037774168E0743003
chr11775008775954E0743974
chr11783166783235E07412132
chr11783370784241E07412336
chr11788757788839E07417723
chr11788895789014E07417861
chr11789029789170E07417995
chr11725421727287E081-43747
chr11775008775954E0813974
chr11778786778866E0817752
chr11778878778990E0817844
chr11779041779261E0818007
chr11782409782544E08111375
chr11782547782587E08111513
chr11782652782712E08111618
chr11782822783126E08111788
chr11783166783235E08112132
chr11783370784241E08112336
chr11784568784701E08113534
chr11785044785136E08114010
chr11785293785337E08114259
chr11787747787803E08116713
chr11787852787935E08116818
chr11787986788159E08116952
chr11788166788267E08117132
chr11788283788451E08117249
chr11788544788603E08117510
chr11788685788733E08117651
chr11788757788839E08117723
chr11788895789014E08117861
chr11789029789170E08117995
chr11790505791483E08119471
chr11794043794710E08123009
chr11794737794810E08123703
chr11811429812418E08140395
chr11749299749351E082-21683
chr11749452749506E082-21528
chr11749789749876E082-21158
chr11749926750044E082-20990
chr11778786778866E0827752
chr11778878778990E0827844
chr11779041779261E0828007
chr11779293779616E0828259
chr11779619779776E0828585
chr11779811779900E0828777
chr11779930780125E0828896
chr11780217780315E0829183
chr11780321780361E0829287
chr11780399780492E0829365
chr11780557780653E0829523
chr11784568784701E08213534
chr11785044785136E08214010
chr11785293785337E08214259
chr11788283788451E08217249
chr11788544788603E08217510
chr11793350794013E08222316
chr11794043794710E08223009
chr11794737794810E08223703
chr11811429812418E08240395










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11746398747953E067-23081
chr11776294778670E0675260
chr11790010790327E06718976
chr11790352790402E06719318
chr11808498810615E06737464
chr11810672810745E06739638
chr11746398747953E068-23081
chr11776294778670E0685260
chr11790010790327E06818976
chr11790352790402E06819318
chr11808498810615E06837464
chr11810672810745E06839638
chr11746398747953E069-23081
chr11776294778670E0695260
chr11790010790327E06918976
chr11790352790402E06919318
chr11808498810615E06937464
chr11810672810745E06939638
chr11746398747953E070-23081
chr11776294778670E0705260
chr11790010790327E07018976
chr11790352790402E07019318
chr11808498810615E07037464
chr11810672810745E07039638
chr11746398747953E071-23081
chr11776294778670E0715260
chr11808498810615E07137464
chr11810672810745E07139638
chr11746398747953E072-23081
chr11776294778670E0725260
chr11790010790327E07218976
chr11790352790402E07219318
chr11808498810615E07237464
chr11810672810745E07239638
chr11746398747953E073-23081
chr11776294778670E0735260
chr11808498810615E07337464
chr11810672810745E07339638
chr11746398747953E074-23081
chr11776294778670E0745260
chr11808498810615E07437464
chr11810672810745E07439638
chr11808498810615E08137464
chr11746398747953E082-23081
chr11776294778670E0825260
chr11790010790327E08218976
chr11790352790402E08219318
chr11808498810615E08237464
chr11810672810745E08239638