rs6983139

Homo sapiens
A>G
CSGALNACT1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0415 (12428/29930,GnomAD)
G=0444 (12935/29118,TOPMED)
A==0497 (2490/5008,1000G)
G=0361 (1391/3854,ALSPAC)
G=0370 (1372/3708,TWINSUK)
chr8:19742818 (GRCh38.p7) (8p21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
144 Enhancers around
17 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 8NC_000008.11:g.19742818A>G
GRCh37.p13 chr 8NC_000008.10:g.19600329A>G

Gene: CSGALNACT1, chondroitin sulfate N-acetylgalactosaminyltransferase 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CSGALNACT1 transcript variant 1NM_001130518.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant 2NM_018371.4:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant 3NR_024040.1:n.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X16XM_006716362.2:c.N/AIntron Variant
CSGALNACT1 transcript variant X16XM_011544584.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X17XM_017013626.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X21XM_017013630.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X22XM_017013631.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X23XM_017013632.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X24XM_017013633.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X25XM_017013634.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X26XM_017013635.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X27XM_017013636.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X28XM_017013637.1:c.N/AIntron Variant
CSGALNACT1 transcript variant X1XM_006716358.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X3XM_006716359.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X7XM_006716360.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X10XM_006716361.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X3XM_006716363.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X14XM_006716364.3:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X4XM_011544578.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X5XM_011544579.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X8XM_011544580.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X9XM_011544582.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X15XM_011544583.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X36XM_011544585.2:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X6XM_017013623.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X11XM_017013624.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X13XM_017013625.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X17XM_017013627.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X19XM_017013628.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X18XM_017013629.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X19XM_017013638.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X35XM_017013639.1:c.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X31XR_001745561.1:n.N/AIntron Variant
CSGALNACT1 transcript variant X33XR_001745563.1:n.N/AIntron Variant
CSGALNACT1 transcript variant X34XR_001745564.1:n.N/AIntron Variant
CSGALNACT1 transcript variant X30XR_001745560.1:n.N/AGenic Upstream Transcript Variant
CSGALNACT1 transcript variant X32XR_001745562.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.495G=0.505
1000GenomesAmericanSub694A=0.500G=0.500
1000GenomesEast AsianSub1008A=0.418G=0.582
1000GenomesEuropeSub1006A=0.586G=0.414
1000GenomesGlobalStudy-wide5008A=0.497G=0.503
1000GenomesSouth AsianSub978A=0.490G=0.510
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.639G=0.361
The Genome Aggregation DatabaseAfricanSub8700A=0.516G=0.484
The Genome Aggregation DatabaseAmericanSub838A=0.520G=0.480
The Genome Aggregation DatabaseEast AsianSub1606A=0.420G=0.580
The Genome Aggregation DatabaseEuropeSub18484A=0.635G=0.364
The Genome Aggregation DatabaseGlobalStudy-wide29930A=0.584G=0.415
The Genome Aggregation DatabaseOtherSub302A=0.540G=0.460
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.555G=0.444
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.630G=0.370
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
rs69831390.000026alcohol dependence(early age of onset)20201924
rs69831390.0000265alcoholismpha002892
rs69831390.000051alcoholismpha002893
rs69831390.000051alcohol dependence20201924

eQTL of rs6983139 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 rs6983139 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 )
chr81958748219588261E067-12068
chr81955478419554863E068-45466
chr81956362019563718E068-36611
chr81956378319563962E068-36367
chr81956415119564203E068-36126
chr81956436819564757E068-35572
chr81956723119567668E068-32661
chr81956790019568005E068-32324
chr81956825719568559E068-31770
chr81957333219573457E068-26872
chr81957351219573827E068-26502
chr81957694419577592E068-22737
chr81957768819577828E068-22501
chr81957790719577967E068-22362
chr81957797319578027E068-22302
chr81957807619578129E068-22200
chr81958548819585852E068-14477
chr81958594019586012E068-14317
chr81958607919586181E068-14148
chr81958748219588261E068-12068
chr81958829519588742E068-11587
chr81959141219591523E068-8806
chr81961593319616340E06815604
chr81962448319624620E06824154
chr81962488119625445E06824552
chr81962553519625724E06825206
chr81962577619625897E06825447
chr81962713519627461E06826806
chr81962751519627565E06827186
chr81955217519552237E069-48092
chr81955246719552756E069-47573
chr81955478419554863E069-45466
chr81957768819577828E069-22501
chr81957790719577967E069-22362
chr81957797319578027E069-22302
chr81957807619578129E069-22200
chr81957821919578321E069-22008
chr81957851219578586E069-21743
chr81958683119587009E069-13320
chr81958702719587371E069-12958
chr81962302119623153E06922692
chr81962448319624620E06924154
chr81962488119625445E06924552
chr81962553519625724E06925206
chr81956790019568005E070-32324
chr81956825719568559E070-31770
chr81956857119568758E070-31571
chr81964592119646885E07045592
chr81955478419554863E071-45466
chr81955490319555005E071-45324
chr81956476019564866E071-35463
chr81958683119587009E071-13320
chr81958702719587371E071-12958
chr81960051619600701E071187
chr81962553519625724E07125206
chr81962577619625897E07125447
chr81962598219626086E07125653
chr81962615919626256E07125830
chr81963697919637482E07136650
chr81957649319576631E072-23698
chr81957694419577592E072-22737
chr81957768819577828E072-22501
chr81958533519585385E072-14944
chr81959103819591269E072-9060
chr81959141219591523E072-8806
chr81961593319616340E07215604
chr81955217519552237E073-48092
chr81955246719552756E073-47573
chr81956825719568559E073-31770
chr81956857119568758E073-31571
chr81957768819577828E073-22501
chr81957790719577967E073-22362
chr81957797319578027E073-22302
chr81957807619578129E073-22200
chr81957821919578321E073-22008
chr81957851219578586E073-21743
chr81960051619600701E073187
chr81962390219623942E07323573
chr81955353219554772E074-45557
chr81955478419554863E074-45466
chr81957797319578027E074-22302
chr81957807619578129E074-22200
chr81957821919578321E074-22008
chr81962448319624620E07424154
chr81962488119625445E07424552
chr81962553519625724E07425206
chr81962577619625897E07425447
chr81962598219626086E07425653
chr81962713519627461E07426806
chr81962751519627565E07427186
chr81955123319551334E081-48995
chr81955133619551386E081-48943
chr81955139519551596E081-48733
chr81955164319552109E081-48220
chr81955217519552237E081-48092
chr81955246719552756E081-47573
chr81955276319552883E081-47446
chr81955290319553082E081-47247
chr81955310219553524E081-46805
chr81955353219554772E081-45557
chr81955490319555005E081-45324
chr81956723119567668E081-32661
chr81956790019568005E081-32324
chr81956825719568559E081-31770
chr81957512619575183E081-25146
chr81957595619576034E081-24295
chr81957622519576487E081-23842
chr81957797319578027E081-22302
chr81957807619578129E081-22200
chr81957821919578321E081-22008
chr81957851219578586E081-21743
chr81957860619578672E081-21657
chr81957868119578765E081-21564
chr81957893319579078E081-21251
chr81960027319600370E0810
chr81960051619600701E081187
chr81960085219600920E081523
chr81955164319552109E082-48220
chr81955217519552237E082-48092
chr81955246719552756E082-47573
chr81955478419554863E082-45466
chr81955490319555005E082-45324
chr81955506319555686E082-44643
chr81955576019555827E082-44502
chr81956723119567668E082-32661
chr81956790019568005E082-32324
chr81956825719568559E082-31770
chr81956857119568758E082-31571
chr81956906619569148E082-31181
chr81957622519576487E082-23842
chr81957649319576631E082-23698
chr81957665119576894E082-23435
chr81957860619578672E082-21657
chr81957868119578765E082-21564
chr81958988119590001E082-10328
chr81959010519590377E082-9952
chr81959058619590636E082-9693
chr81959081219590877E082-9452
chr81959103819591269E082-9060
chr81960027319600370E0820
chr81960051619600701E082187
chr81960085219600920E082523
chr81960100819601075E082679
chr81960171219601973E0821383










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr81961334819613657E06713019
chr81961376219615904E06713433
chr81961334819613657E06813019
chr81961376219615904E06813433
chr81961334819613657E06913019
chr81961376219615904E06913433
chr81961334819613657E07113019
chr81961376219615904E07113433
chr81961334819613657E07213019
chr81961376219615904E07213433
chr81961334819613657E07313019
chr81961376219615904E07313433
chr81961334819613657E07413019
chr81961376219615904E07413433
chr81961334819613657E08113019
chr81961334819613657E08213019
chr81961376219615904E08213433