rs10779824

Homo sapiens
C>T
GALNT2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0280 (8387/29860,GnomAD)
T=0304 (8867/29116,TOPMED)
T=0269 (1348/5008,1000G)
T=0289 (1112/3854,ALSPAC)
T=0277 (1027/3708,TWINSUK)
chr1:230095509 (GRCh38.p7) (1q42.13)
AD
GWASdb2
2   publication(s)
See rs on genome

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.230095509C>T
GRCh37.p13 chr 1NC_000001.10:g.230231256C>T
GALNT2 RefSeqGeneNG_011854.2:g.42721C>T

Gene: GALNT2, polypeptide N-acetylgalactosaminyltransferase 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GALNT2 transcript variant 2NM_001291866.1:c.N/AIntron Variant
GALNT2 transcript variant 1NM_004481.4:c.N/AIntron Variant
GALNT2 transcript variant 3NR_120373.1:n.N/AGenic Downstream Transcript Variant
GALNT2 transcript variant X1XM_017000963.1:c.N/AIntron Variant
GALNT2 transcript variant X3XM_017000965.1:c.N/AIntron Variant
GALNT2 transcript variant X2XM_017000964.1:c.N/AGenic Upstream Transcript Variant
GALNT2 transcript variant X4XM_017000966.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.652T=0.348
1000GenomesAmericanSub694C=0.790T=0.210
1000GenomesEast AsianSub1008C=0.728T=0.272
1000GenomesEuropeSub1006C=0.745T=0.255
1000GenomesGlobalStudy-wide5008C=0.731T=0.269
1000GenomesSouth AsianSub978C=0.790T=0.210
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.711T=0.289
The Genome Aggregation DatabaseAfricanSub8694C=0.678T=0.322
The Genome Aggregation DatabaseAmericanSub836C=0.790T=0.210
The Genome Aggregation DatabaseEast AsianSub1598C=0.745T=0.255
The Genome Aggregation DatabaseEuropeSub18432C=0.732T=0.267
The Genome Aggregation DatabaseGlobalStudy-wide29860C=0.719T=0.280
The Genome Aggregation DatabaseOtherSub300C=0.760T=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.695T=0.304
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.723T=0.277
PMID Title Author Journal
28155865A Genome-Wide Association Study Identifies Genetic Variants Associated with Mathematics Ability.Chen HSci Rep
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs107798245.72E-05alcohol consumption23743675

eQTL of rs10779824 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 rs10779824 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 )
chr1230205242230205367E067-25889
chr1230205623230205896E067-25360
chr1230207835230207885E067-23371
chr1230208117230208319E067-22937
chr1230208638230208707E067-22549
chr1230208726230208848E067-22408
chr1230208917230208977E067-22279
chr1230209178230209553E067-21703
chr1230209632230209814E067-21442
chr1230210111230210246E067-21010
chr1230215040230216846E067-14410
chr1230219733230221171E067-10085
chr1230222505230222555E067-8701
chr1230222565230222615E067-8641
chr1230238650230238786E0677394
chr1230238957230239034E0677701
chr1230239370230239686E0678114
chr1230239701230239859E0678445
chr1230239912230240025E0678656
chr1230240136230242131E0678880
chr1230242423230242500E06711167
chr1230242543230242593E06711287
chr1230246923230247094E06715667
chr1230247258230247368E06716002
chr1230247402230247560E06716146
chr1230247694230248493E06716438
chr1230248506230250331E06717250
chr1230251446230251597E06720190
chr1230251746230251796E06720490
chr1230256319230256482E06725063
chr1230256504230257063E06725248
chr1230257172230257273E06725916
chr1230260456230261070E06729200
chr1230261081230261236E06729825
chr1230263513230263750E06732257
chr1230263887230264054E06732631
chr1230266014230266117E06734758
chr1230266292230266354E06735036
chr1230273165230273281E06741909
chr1230273350230273469E06742094
chr1230275621230275756E06744365
chr1230276002230276148E06744746
chr1230276175230276506E06744919
chr1230276641230276999E06745385
chr1230277872230277932E06746616
chr1230278006230278067E06746750
chr1230278124230278174E06746868
chr1230278470230278726E06747214
chr1230278741230278873E06747485
chr1230279096230279356E06747840
chr1230279369230279618E06748113
chr1230279813230280066E06748557
chr1230280116230280180E06748860
chr1230280307230280427E06749051
chr1230280597230280835E06749341
chr1230280971230281078E06749715
chr1230281116230281203E06749860
chr1230205623230205896E068-25360
chr1230206314230206398E068-24858
chr1230206424230206478E068-24778
chr1230207163230207213E068-24043
chr1230207274230207415E068-23841
chr1230208638230208707E068-22549
chr1230208726230208848E068-22408
chr1230208917230208977E068-22279
chr1230209178230209553E068-21703
chr1230209632230209814E068-21442
chr1230210111230210246E068-21010
chr1230210564230210685E068-20571
chr1230210759230210821E068-20435
chr1230211343230211393E068-19863
chr1230212014230212098E068-19158
chr1230213366230213493E068-17763
chr1230213532230213703E068-17553
chr1230213714230213843E068-17413
chr1230215040230216846E068-14410
chr1230219733230221171E068-10085
chr1230222565230222615E068-8641
chr1230222669230223245E068-8011
chr1230237687230237822E0686431
chr1230237897230238048E0686641
chr1230239370230239686E0688114
chr1230239701230239859E0688445
chr1230239912230240025E0688656
chr1230240136230242131E0688880
chr1230246923230247094E06815667
chr1230247258230247368E06816002
chr1230247402230247560E06816146
chr1230252888230253244E06821632
chr1230253410230253460E06822154
chr1230253563230253729E06822307
chr1230256319230256482E06825063
chr1230256504230257063E06825248
chr1230257172230257273E06825916
chr1230260176230260263E06828920
chr1230260456230261070E06829200
chr1230261081230261236E06829825
chr1230261391230261673E06830135
chr1230261716230262029E06830460
chr1230262152230262238E06830896
chr1230262388230262438E06831132
chr1230263513230263750E06832257
chr1230263887230264054E06832631
chr1230273165230273281E06841909
chr1230273350230273469E06842094
chr1230275265230275336E06844009
chr1230275621230275756E06844365
chr1230276641230276999E06845385
chr1230278006230278067E06846750
chr1230278124230278174E06846868
chr1230278470230278726E06847214
chr1230278741230278873E06847485
chr1230279096230279356E06847840
chr1230279369230279618E06848113
chr1230279813230280066E06848557
chr1230280116230280180E06848860
chr1230280307230280427E06849051
chr1230280597230280835E06849341
chr1230280971230281078E06849715
chr1230281116230281203E06849860
chr1230205242230205367E069-25889
chr1230205623230205896E069-25360
chr1230208638230208707E069-22549
chr1230208726230208848E069-22408
chr1230208917230208977E069-22279
chr1230209178230209553E069-21703
chr1230209632230209814E069-21442
chr1230210111230210246E069-21010
chr1230219733230221171E069-10085
chr1230222131230222422E069-8834
chr1230222505230222555E069-8701
chr1230222565230222615E069-8641
chr1230239370230239686E0698114
chr1230239701230239859E0698445
chr1230239912230240025E0698656
chr1230240136230242131E0698880
chr1230242423230242500E06911167
chr1230242543230242593E06911287
chr1230246923230247094E06915667
chr1230247258230247368E06916002
chr1230247402230247560E06916146
chr1230247694230248493E06916438
chr1230251446230251597E06920190
chr1230251746230251796E06920490
chr1230253410230253460E06922154
chr1230253563230253729E06922307
chr1230256319230256482E06925063
chr1230256504230257063E06925248
chr1230260456230261070E06929200
chr1230261081230261236E06929825
chr1230263887230264054E06932631
chr1230264653230265021E06933397
chr1230266014230266117E06934758
chr1230266292230266354E06935036
chr1230272050230272154E06940794
chr1230273165230273281E06941909
chr1230273350230273469E06942094
chr1230275265230275336E06944009
chr1230275621230275756E06944365
chr1230276641230276999E06945385
chr1230277872230277932E06946616
chr1230278006230278067E06946750
chr1230278124230278174E06946868
chr1230278470230278726E06947214
chr1230278741230278873E06947485
chr1230279096230279356E06947840
chr1230279369230279618E06948113
chr1230279813230280066E06948557
chr1230280116230280180E06948860
chr1230280307230280427E06949051
chr1230280597230280835E06949341
chr1230280971230281078E06949715
chr1230281116230281203E06949860
chr1230205623230205896E070-25360
chr1230206314230206398E070-24858
chr1230208726230208848E070-22408
chr1230208917230208977E070-22279
chr1230209178230209553E070-21703
chr1230209632230209814E070-21442
chr1230210111230210246E070-21010
chr1230210564230210685E070-20571
chr1230214780230214885E070-16371
chr1230219733230221171E070-10085
chr1230221933230222023E070-9233
chr1230222131230222422E070-8834
chr1230222505230222555E070-8701
chr1230222565230222615E070-8641
chr1230222669230223245E070-8011
chr1230238957230239034E0707701
chr1230239370230239686E0708114
chr1230239701230239859E0708445
chr1230239912230240025E0708656
chr1230240136230242131E0708880
chr1230246923230247094E07015667
chr1230247258230247368E07016002
chr1230247402230247560E07016146
chr1230247694230248493E07016438
chr1230248506230250331E07017250
chr1230260456230261070E07029200
chr1230261081230261236E07029825
chr1230261391230261673E07030135
chr1230273350230273469E07042094
chr1230274554230274720E07043298
chr1230275265230275336E07044009
chr1230275621230275756E07044365
chr1230276002230276148E07044746
chr1230276175230276506E07044919
chr1230276641230276999E07045385
chr1230278006230278067E07046750
chr1230278124230278174E07046868
chr1230278470230278726E07047214
chr1230278741230278873E07047485
chr1230279096230279356E07047840
chr1230279369230279618E07048113
chr1230279813230280066E07048557
chr1230280116230280180E07048860
chr1230280307230280427E07049051
chr1230280597230280835E07049341
chr1230280971230281078E07049715
chr1230281116230281203E07049860
chr1230205242230205367E071-25889
chr1230205623230205896E071-25360
chr1230206314230206398E071-24858
chr1230206424230206478E071-24778
chr1230207163230207213E071-24043
chr1230207274230207415E071-23841
chr1230207516230207685E071-23571
chr1230207835230207885E071-23371
chr1230208117230208319E071-22937
chr1230208638230208707E071-22549
chr1230208726230208848E071-22408
chr1230208917230208977E071-22279
chr1230209178230209553E071-21703
chr1230209632230209814E071-21442
chr1230210111230210246E071-21010
chr1230210564230210685E071-20571
chr1230210759230210821E071-20435
chr1230211343230211393E071-19863
chr1230214780230214885E071-16371
chr1230219733230221171E071-10085
chr1230221933230222023E071-9233
chr1230222131230222422E071-8834
chr1230222505230222555E071-8701
chr1230222565230222615E071-8641
chr1230222669230223245E071-8011
chr1230232591230232646E0711335
chr1230238957230239034E0717701
chr1230239370230239686E0718114
chr1230239701230239859E0718445
chr1230239912230240025E0718656
chr1230240136230242131E0718880
chr1230245618230246272E07114362
chr1230246923230247094E07115667
chr1230247258230247368E07116002
chr1230247402230247560E07116146
chr1230255819230255873E07124563
chr1230255897230256272E07124641
chr1230256319230256482E07125063
chr1230260176230260263E07128920
chr1230260456230261070E07129200
chr1230261081230261236E07129825
chr1230261391230261673E07130135
chr1230261716230262029E07130460
chr1230262152230262238E07130896
chr1230262388230262438E07131132
chr1230262712230263094E07131456
chr1230263513230263750E07132257
chr1230263887230264054E07132631
chr1230264653230265021E07133397
chr1230266014230266117E07134758
chr1230272050230272154E07140794
chr1230273350230273469E07142094
chr1230275265230275336E07144009
chr1230275621230275756E07144365
chr1230276002230276148E07144746
chr1230276175230276506E07144919
chr1230276641230276999E07145385
chr1230277872230277932E07146616
chr1230278006230278067E07146750
chr1230278124230278174E07146868
chr1230278470230278726E07147214
chr1230278741230278873E07147485
chr1230279813230280066E07148557
chr1230280116230280180E07148860
chr1230280307230280427E07149051
chr1230280597230280835E07149341
chr1230280971230281078E07149715
chr1230281116230281203E07149860
chr1230208117230208319E072-22937
chr1230208638230208707E072-22549
chr1230208726230208848E072-22408
chr1230208917230208977E072-22279
chr1230209178230209553E072-21703
chr1230209632230209814E072-21442
chr1230210111230210246E072-21010
chr1230210564230210685E072-20571
chr1230210759230210821E072-20435
chr1230213532230213703E072-17553
chr1230219733230221171E072-10085
chr1230222505230222555E072-8701
chr1230222565230222615E072-8641
chr1230222669230223245E072-8011
chr1230238957230239034E0727701
chr1230239370230239686E0728114
chr1230239701230239859E0728445
chr1230245618230246272E07214362
chr1230246923230247094E07215667
chr1230247258230247368E07216002
chr1230247402230247560E07216146
chr1230251446230251597E07220190
chr1230251746230251796E07220490
chr1230260176230260263E07228920
chr1230260456230261070E07229200
chr1230261081230261236E07229825
chr1230272050230272154E07240794
chr1230273165230273281E07241909
chr1230273350230273469E07242094
chr1230275265230275336E07244009
chr1230275621230275756E07244365
chr1230276002230276148E07244746
chr1230276175230276506E07244919
chr1230276641230276999E07245385
chr1230277108230277260E07245852
chr1230277872230277932E07246616
chr1230278006230278067E07246750
chr1230278124230278174E07246868
chr1230278470230278726E07247214
chr1230278741230278873E07247485
chr1230279096230279356E07247840
chr1230279369230279618E07248113
chr1230279813230280066E07248557
chr1230280116230280180E07248860
chr1230280307230280427E07249051
chr1230280597230280835E07249341
chr1230280971230281078E07249715
chr1230281116230281203E07249860
chr1230205242230205367E073-25889
chr1230205623230205896E073-25360
chr1230206314230206398E073-24858
chr1230207163230207213E073-24043
chr1230207274230207415E073-23841
chr1230207516230207685E073-23571
chr1230208638230208707E073-22549
chr1230208726230208848E073-22408
chr1230208917230208977E073-22279
chr1230209178230209553E073-21703
chr1230209632230209814E073-21442
chr1230210111230210246E073-21010
chr1230210564230210685E073-20571
chr1230210759230210821E073-20435
chr1230219733230221171E073-10085
chr1230222669230223245E073-8011
chr1230237687230237822E0736431
chr1230237897230238048E0736641
chr1230238957230239034E0737701
chr1230239370230239686E0738114
chr1230239701230239859E0738445
chr1230239912230240025E0738656
chr1230240136230242131E0738880
chr1230242423230242500E07311167
chr1230242543230242593E07311287
chr1230245618230246272E07314362
chr1230246923230247094E07315667
chr1230247258230247368E07316002
chr1230247402230247560E07316146
chr1230247694230248493E07316438
chr1230248506230250331E07317250
chr1230256319230256482E07325063
chr1230256504230257063E07325248
chr1230257172230257273E07325916
chr1230260456230261070E07329200
chr1230261081230261236E07329825
chr1230261391230261673E07330135
chr1230261716230262029E07330460
chr1230262152230262238E07330896
chr1230263887230264054E07332631
chr1230266292230266354E07335036
chr1230266413230266558E07335157
chr1230272050230272154E07340794
chr1230275265230275336E07344009
chr1230275621230275756E07344365
chr1230278006230278067E07346750
chr1230278124230278174E07346868
chr1230278470230278726E07347214
chr1230278741230278873E07347485
chr1230279096230279356E07347840
chr1230279369230279618E07348113
chr1230279813230280066E07348557
chr1230280116230280180E07348860
chr1230280307230280427E07349051
chr1230280597230280835E07349341
chr1230280971230281078E07349715
chr1230281116230281203E07349860
chr1230205242230205367E074-25889
chr1230205623230205896E074-25360
chr1230206314230206398E074-24858
chr1230206424230206478E074-24778
chr1230207163230207213E074-24043
chr1230207274230207415E074-23841
chr1230208638230208707E074-22549
chr1230208726230208848E074-22408
chr1230208917230208977E074-22279
chr1230209178230209553E074-21703
chr1230209632230209814E074-21442
chr1230210111230210246E074-21010
chr1230210564230210685E074-20571
chr1230210759230210821E074-20435
chr1230212575230212692E074-18564
chr1230212814230212897E074-18359
chr1230212905230213365E074-17891
chr1230213366230213493E074-17763
chr1230219733230221171E074-10085
chr1230221933230222023E074-9233
chr1230222131230222422E074-8834
chr1230222505230222555E074-8701
chr1230222565230222615E074-8641
chr1230239701230239859E0748445
chr1230239912230240025E0748656
chr1230240136230242131E0748880
chr1230243878230243934E07412622
chr1230245618230246272E07414362
chr1230246923230247094E07415667
chr1230247258230247368E07416002
chr1230247402230247560E07416146
chr1230247694230248493E07416438
chr1230255897230256272E07424641
chr1230256319230256482E07425063
chr1230256504230257063E07425248
chr1230260176230260263E07428920
chr1230260456230261070E07429200
chr1230261081230261236E07429825
chr1230261391230261673E07430135
chr1230261716230262029E07430460
chr1230262152230262238E07430896
chr1230262388230262438E07431132
chr1230263513230263750E07432257
chr1230263887230264054E07432631
chr1230272050230272154E07440794
chr1230272208230272708E07440952
chr1230273350230273469E07442094
chr1230275621230275756E07444365
chr1230276641230276999E07445385
chr1230277108230277260E07445852
chr1230277872230277932E07446616
chr1230278006230278067E07446750
chr1230278124230278174E07446868
chr1230278470230278726E07447214
chr1230278741230278873E07447485
chr1230279096230279356E07447840
chr1230279369230279618E07448113
chr1230279813230280066E07448557
chr1230280116230280180E07448860
chr1230280307230280427E07449051
chr1230280597230280835E07449341
chr1230280971230281078E07449715
chr1230281116230281203E07449860
chr1230205242230205367E081-25889
chr1230205623230205896E081-25360
chr1230208638230208707E081-22549
chr1230208726230208848E081-22408
chr1230208917230208977E081-22279
chr1230209178230209553E081-21703
chr1230209632230209814E081-21442
chr1230210111230210246E081-21010
chr1230210564230210685E081-20571
chr1230210759230210821E081-20435
chr1230219733230221171E081-10085
chr1230232591230232646E0811335
chr1230234882230234932E0813626
chr1230236787230236887E0815531
chr1230237001230237062E0815745
chr1230237370230237414E0816114
chr1230238650230238786E0817394
chr1230238957230239034E0817701
chr1230239370230239686E0818114
chr1230239701230239859E0818445
chr1230239912230240025E0818656
chr1230240136230242131E0818880
chr1230242423230242500E08111167
chr1230242543230242593E08111287
chr1230242784230243065E08111528
chr1230246923230247094E08115667
chr1230247258230247368E08116002
chr1230247402230247560E08116146
chr1230247694230248493E08116438
chr1230257853230258019E08126597
chr1230258061230258847E08126805
chr1230259978230260175E08128722
chr1230260176230260263E08128920
chr1230260456230261070E08129200
chr1230261081230261236E08129825
chr1230261391230261673E08130135
chr1230261716230262029E08130460
chr1230262152230262238E08130896
chr1230262388230262438E08131132
chr1230262712230263094E08131456
chr1230263513230263750E08132257
chr1230263887230264054E08132631
chr1230264653230265021E08133397
chr1230266014230266117E08134758
chr1230266292230266354E08135036
chr1230266413230266558E08135157
chr1230272050230272154E08140794
chr1230272208230272708E08140952
chr1230272780230273084E08141524
chr1230273165230273281E08141909
chr1230273350230273469E08142094
chr1230275621230275756E08144365
chr1230276002230276148E08144746
chr1230276175230276506E08144919
chr1230276641230276999E08145385
chr1230277108230277260E08145852
chr1230277872230277932E08146616
chr1230278006230278067E08146750
chr1230278124230278174E08146868
chr1230278470230278726E08147214
chr1230278741230278873E08147485
chr1230279096230279356E08147840
chr1230279369230279618E08148113
chr1230280597230280835E08149341
chr1230280971230281078E08149715
chr1230281116230281203E08149860
chr1230211343230211393E082-19863
chr1230222669230223245E082-8011
chr1230238957230239034E0827701
chr1230239370230239686E0828114
chr1230239701230239859E0828445
chr1230239912230240025E0828656
chr1230246923230247094E08215667
chr1230247258230247368E08216002
chr1230247402230247560E08216146
chr1230247694230248493E08216438
chr1230257172230257273E08225916
chr1230257385230257439E08226129
chr1230257853230258019E08226597
chr1230258061230258847E08226805
chr1230258871230259489E08227615
chr1230260456230261070E08229200
chr1230261081230261236E08229825
chr1230263513230263750E08232257
chr1230263887230264054E08232631
chr1230264653230265021E08233397
chr1230272780230273084E08241524
chr1230273165230273281E08241909
chr1230273350230273469E08242094
chr1230277108230277260E08245852
chr1230277872230277932E08246616
chr1230278006230278067E08246750
chr1230278124230278174E08246868
chr1230278470230278726E08247214
chr1230278741230278873E08247485
chr1230279096230279356E08247840
chr1230279369230279618E08248113
chr1230279813230280066E08248557
chr1230280116230280180E08248860










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1230202170230204968E067-26288
chr1230202170230204968E068-26288
chr1230202170230204968E069-26288
chr1230202170230204968E070-26288
chr1230202170230204968E071-26288
chr1230202170230204968E072-26288
chr1230202170230204968E073-26288
chr1230202170230204968E074-26288
chr1230202170230204968E081-26288
chr1230202170230204968E082-26288