rs7969300

Homo sapiens
C>T
ATXN2 : Missense Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0090 (10211/112792,ExAC)
T=0071 (2134/29956,GnomAD)
T=0071 (2072/29118,TOPMED)
C==0043 (560/13004,GO-ESP)
T=0180 (899/5008,1000G)
T=0004 (15/3854,ALSPAC)
T=0003 (10/3708,TWINSUK)
chr12:111555908 (GRCh38.p7) (12q24.12)
AD
GWASdb2
2   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.111555908C>T
GRCh37.p13 chr 12NC_000012.11:g.111993712C>T
ATXN2 RefSeqGeneNG_011572.2:g.48769G>A

Gene: ATXN2, ataxin 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ATXN2 transcript variant 3NM_001310123.1:c.N/AIntron Variant
ATXN2 transcript variant 2NM_001310121.1:c.N/A5 Prime UTR Variant
ATXN2 transcript variant 1NM_002973.3:c.743G>AS [AGT]> N [AAT]Coding Sequence Variant
ataxin-2 isoform 1NP_002964.3:p.Ser...NP_002964.3:p.Ser248AsnS [Ser]> N [Asn]Missense Variant
ATXN2 transcript variant 4NR_132311.1:n.905G>AG>ANon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.849T=0.151
1000GenomesAmericanSub694C=0.880T=0.120
1000GenomesEast AsianSub1008C=0.477T=0.523
1000GenomesEuropeSub1006C=0.998T=0.002
1000GenomesGlobalStudy-wide5008C=0.820T=0.180
1000GenomesSouth AsianSub978C=0.910T=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.996T=0.004
The Exome Aggregation ConsortiumAmericanSub20984C=0.830T=0.169
The Exome Aggregation ConsortiumAsianSub24036C=0.736T=0.263
The Exome Aggregation ConsortiumEuropeSub66912C=0.995T=0.004
The Exome Aggregation ConsortiumGlobalStudy-wide112792C=0.909T=0.090
The Exome Aggregation ConsortiumOtherSub860C=0.950T=0.050
The Genome Aggregation DatabaseAfricanSub8708C=0.882T=0.118
The Genome Aggregation DatabaseAmericanSub838C=0.850T=0.150
The Genome Aggregation DatabaseEast AsianSub1606C=0.425T=0.575
The Genome Aggregation DatabaseEuropeSub18502C=0.996T=0.003
The Genome Aggregation DatabaseGlobalStudy-wide29956C=0.928T=0.071
The Genome Aggregation DatabaseOtherSub302C=0.990T=0.010
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.928T=0.071
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.997T=0.003
PMID Title Author Journal
23555315Genome-wide testing of putative functional exonic variants in relationship with breast and prostate cancer risk in a multiethnic population.Haiman CAPLoS Genet
24333172Association analysis of a functional variant in ATXN2 with schizophrenia.Zhang FNeurosci Lett

P-Value

SNP ID p-value Traits Study
rs79693002.73E-19alcohol (ever vs. never)23555315

eQTL of rs7969300 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 rs7969300 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 )
chr12111964831111965022E067-28690
chr12111965054111965120E067-28592
chr12111965328111965388E067-28324
chr12111965441111965571E067-28141
chr12111986577111986627E067-7085
chr12111986804111986854E067-6858
chr12111994089111994153E067377
chr12111994238111994324E067526
chr12111995075111995277E0671363
chr12111995315111995599E0671603
chr12111998386111998436E0674674
chr12111998439111998544E0674727
chr12111998569111998626E0674857
chr12112006408112006448E06712696
chr12112006565112006730E06712853
chr12112006871112007047E06713159
chr12112007090112007157E06713378
chr12112007223112007484E06713511
chr12112007565112007664E06713853
chr12112007679112007719E06713967
chr12112007759112007843E06714047
chr12112007864112008170E06714152
chr12112008243112008407E06714531
chr12112008422112008670E06714710
chr12112008735112008859E06715023
chr12112011088112011434E06717376
chr12112031803112032075E06738091
chr12112032345112032406E06738633
chr12112032644112032750E06738932
chr12112032894112032954E06739182
chr12112033098112033182E06739386
chr12112033290112033361E06739578
chr12112033588112033662E06739876
chr12112033968112034040E06740256
chr12112034042112034135E06740330
chr12111964831111965022E068-28690
chr12111965054111965120E068-28592
chr12111965328111965388E068-28324
chr12111965441111965571E068-28141
chr12111995075111995277E0681363
chr12111995315111995599E0681603
chr12111998386111998436E0684674
chr12111998439111998544E0684727
chr12111998569111998626E0684857
chr12112006408112006448E06812696
chr12112006565112006730E06812853
chr12112006871112007047E06813159
chr12112007864112008170E06814152
chr12112008243112008407E06814531
chr12112008422112008670E06814710
chr12112018247112018294E06824535
chr12112019506112019703E06825794
chr12112019896112019982E06826184
chr12112025325112025414E06831613
chr12112025416112025846E06831704
chr12112031803112032075E06838091
chr12112032345112032406E06838633
chr12112032644112032750E06838932
chr12112032894112032954E06839182
chr12112033290112033361E06839578
chr12112033588112033662E06839876
chr12112033968112034040E06840256
chr12112034042112034135E06840330
chr12111964831111965022E069-28690
chr12111965054111965120E069-28592
chr12111965328111965388E069-28324
chr12111965441111965571E069-28141
chr12111986577111986627E069-7085
chr12111995075111995277E0691363
chr12111995315111995599E0691603
chr12111995661111995851E0691949
chr12112006408112006448E06912696
chr12112006565112006730E06912853
chr12112006871112007047E06913159
chr12112007090112007157E06913378
chr12112007223112007484E06913511
chr12112008243112008407E06914531
chr12112008422112008670E06914710
chr12112019506112019703E06925794
chr12112019896112019982E06926184
chr12112020172112020212E06926460
chr12112032894112032954E06939182
chr12112033098112033182E06939386
chr12112033290112033361E06939578
chr12112033588112033662E06939876
chr12112033968112034040E06940256
chr12112034042112034135E06940330
chr12112008422112008670E07014710
chr12112031803112032075E07038091
chr12112033098112033182E07039386
chr12112033290112033361E07039578
chr12111964831111965022E071-28690
chr12111965054111965120E071-28592
chr12111965328111965388E071-28324
chr12111965441111965571E071-28141
chr12111986011111986150E071-7562
chr12111986577111986627E071-7085
chr12111995075111995277E0711363
chr12111995315111995599E0711603
chr12111998386111998436E0714674
chr12111998439111998544E0714727
chr12111998569111998626E0714857
chr12111998717111998777E0715005
chr12111998880111998930E0715168
chr12112006408112006448E07112696
chr12112006565112006730E07112853
chr12112006871112007047E07113159
chr12112007090112007157E07113378
chr12112007223112007484E07113511
chr12112007565112007664E07113853
chr12112007679112007719E07113967
chr12112007759112007843E07114047
chr12112007864112008170E07114152
chr12112008243112008407E07114531
chr12112008422112008670E07114710
chr12112008735112008859E07115023
chr12112008903112008973E07115191
chr12112009162112009264E07115450
chr12112019328112019453E07125616
chr12112019506112019703E07125794
chr12112031803112032075E07138091
chr12112032345112032406E07138633
chr12112032644112032750E07138932
chr12112032894112032954E07139182
chr12112033098112033182E07139386
chr12112033968112034040E07140256
chr12112034042112034135E07140330
chr12111964831111965022E072-28690
chr12111965054111965120E072-28592
chr12111965328111965388E072-28324
chr12111965441111965571E072-28141
chr12111998386111998436E0724674
chr12111998439111998544E0724727
chr12111998569111998626E0724857
chr12112006408112006448E07212696
chr12112006565112006730E07212853
chr12112007223112007484E07213511
chr12112007565112007664E07213853
chr12112007679112007719E07213967
chr12112007759112007843E07214047
chr12112007864112008170E07214152
chr12112008243112008407E07214531
chr12112008422112008670E07214710
chr12112019328112019453E07225616
chr12112019506112019703E07225794
chr12112033098112033182E07239386
chr12112033968112034040E07240256
chr12112034042112034135E07240330
chr12111964831111965022E073-28690
chr12111965054111965120E073-28592
chr12111965328111965388E073-28324
chr12111965441111965571E073-28141
chr12112006408112006448E07312696
chr12112006565112006730E07312853
chr12112006871112007047E07313159
chr12112007090112007157E07313378
chr12112007223112007484E07313511
chr12112007565112007664E07313853
chr12112007679112007719E07313967
chr12112007759112007843E07314047
chr12112007864112008170E07314152
chr12112015973112016618E07322261
chr12112033098112033182E07339386
chr12112033290112033361E07339578
chr12112033588112033662E07339876
chr12112033968112034040E07340256
chr12112034042112034135E07340330
chr12111964831111965022E074-28690
chr12111965054111965120E074-28592
chr12111965328111965388E074-28324
chr12111965441111965571E074-28141
chr12111994089111994153E074377
chr12111994238111994324E074526
chr12111995075111995277E0741363
chr12111995315111995599E0741603
chr12111995661111995851E0741949
chr12112006871112007047E07413159
chr12112007090112007157E07413378
chr12112007223112007484E07413511
chr12112007565112007664E07413853
chr12112007679112007719E07413967
chr12112007759112007843E07414047
chr12112007864112008170E07414152
chr12112008243112008407E07414531
chr12112008422112008670E07414710
chr12112008735112008859E07415023
chr12112019328112019453E07425616
chr12112019506112019703E07425794
chr12112031179112031219E07437467
chr12112031250112031389E07437538
chr12112031424112031568E07437712
chr12112031803112032075E07438091
chr12112032345112032406E07438633
chr12112032644112032750E07438932
chr12112032894112032954E07439182
chr12112033098112033182E07439386
chr12112033290112033361E07439578
chr12112033588112033662E07439876
chr12112033968112034040E07440256
chr12112034042112034135E07440330
chr12111994238111994324E081526
chr12112030760112030905E08137048
chr12112031424112031568E08137712
chr12112031803112032075E08138091
chr12112033098112033182E08139386
chr12112033290112033361E08139578
chr12112033588112033662E08139876
chr12112033968112034040E08140256
chr12112034042112034135E08140330
chr12112031803112032075E08238091










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr12112034840112038369E06741128
chr12112034840112038369E06841128
chr12112034840112038369E06941128
chr12112034840112038369E07041128
chr12112034840112038369E07141128
chr12112034840112038369E07241128
chr12112034840112038369E07341128
chr12112034840112038369E07441128
chr12112034840112038369E08141128
chr12112034840112038369E08241128