rs11238042

Homo sapiens
G>A
SHANK2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0229 (6865/29938,GnomAD)
A=0182 (5307/29118,TOPMED)
A=0212 (1060/5008,1000G)
A=0303 (1167/3854,ALSPAC)
A=0311 (1153/3708,TWINSUK)
chr11:70942895 (GRCh38.p7) (11q13.4)
AD
GWASdb2
1   publication(s)
See rs on genome
263 Enhancers around
36 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.70942895G>A
GRCh37.p13 chr 11 fix patch HG865_PATCHNW_004070871.1:g.487108G>A
GRCh37.p13 chr 11NC_000011.9:g.70789000G>A

Gene: SHANK2, SH3 and multiple ankyrin repeat domains 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SHANK2 transcript variant 1NM_012309.4:c.N/AIntron Variant
SHANK2 transcript variant 2NM_133266.4:c.N/AGenic Upstream Transcript Variant
SHANK2 transcript variant 3NR_110766.1:n.N/AGenic Upstream Transcript Variant
SHANK2 transcript variant X1XM_017017387.1:c.N/AIntron Variant
SHANK2 transcript variant X2XM_017017388.1:c.N/AIntron Variant
SHANK2 transcript variant X3XM_017017389.1:c.N/AIntron Variant
SHANK2 transcript variant X4XM_005277932.3:c.N/AGenic Upstream Transcript Variant
SHANK2 transcript variant X5XM_017017390.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.979A=0.021
1000GenomesAmericanSub694G=0.780A=0.220
1000GenomesEast AsianSub1008G=0.690A=0.310
1000GenomesEuropeSub1006G=0.710A=0.290
1000GenomesGlobalStudy-wide5008G=0.788A=0.212
1000GenomesSouth AsianSub978G=0.720A=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.697A=0.303
The Genome Aggregation DatabaseAfricanSub8728G=0.943A=0.057
The Genome Aggregation DatabaseAmericanSub838G=0.760A=0.240
The Genome Aggregation DatabaseEast AsianSub1612G=0.718A=0.282
The Genome Aggregation DatabaseEuropeSub18458G=0.694A=0.306
The Genome Aggregation DatabaseGlobalStudy-wide29938G=0.770A=0.229
The Genome Aggregation DatabaseOtherSub302G=0.810A=0.190
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.817A=0.182
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.689A=0.311
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs112380425.2E-05alcoholism (heaviness of drinking)21529783

eQTL of rs11238042 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 rs11238042 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 )
chr11449140449294E067-37814
chr11451917451975E067-35133
chr11470287470555E067-16553
chr11476036476111E067-10997
chr11476189476245E067-10863
chr11476501476590E067-10518
chr11476777476837E067-10271
chr11477085477135E067-9973
chr11477159477329E067-9779
chr11477457477585E067-9523
chr11479158479332E067-7776
chr11479455479574E067-7534
chr11494512494631E0677404
chr11494697495232E0677589
chr11495269495499E0678161
chr11495547495630E0678439
chr11495663496075E0678555
chr11496162496265E0679054
chr11496298496347E0679190
chr11499603499701E06712495
chr11499719499778E06712611
chr11499830499904E06712722
chr11501848501898E06714740
chr11502035502126E06714927
chr11502174502387E06715066
chr11502430502826E06715322
chr11502859503105E06715751
chr11534033534130E06746925
chr11443545443981E068-43127
chr11451917451975E068-35133
chr11468203468961E068-18147
chr11468994469034E068-18074
chr11494370494468E0687262
chr11494512494631E0687404
chr11494697495232E0687589
chr11495269495499E0688161
chr11495547495630E0688439
chr11501478501825E06814370
chr11501848501898E06814740
chr11502035502126E06814927
chr11502174502387E06815066
chr11502430502826E06815322
chr11502859503105E06815751
chr11451917451975E069-35133
chr11452027452531E069-34577
chr11452536452752E069-34356
chr11476036476111E069-10997
chr11476189476245E069-10863
chr11476501476590E069-10518
chr11476777476837E069-10271
chr11477085477135E069-9973
chr11477159477329E069-9779
chr11477457477585E069-9523
chr11477755477862E069-9246
chr11479158479332E069-7776
chr11479455479574E069-7534
chr11493906494047E0696798
chr11494058494130E0696950
chr11494241494313E0697133
chr11494370494468E0697262
chr11494512494631E0697404
chr11494697495232E0697589
chr11495269495499E0698161
chr11495547495630E0698439
chr11495663496075E0698555
chr11496162496265E0699054
chr11496298496347E0699190
chr11498278498426E06911170
chr11498451498524E06911343
chr11498529498628E06911421
chr11498693499250E06911585
chr11499324499461E06912216
chr11499488499581E06912380
chr11499603499701E06912495
chr11499719499778E06912611
chr11499830499904E06912722
chr11500379500437E06913271
chr11501848501898E06914740
chr11502174502387E06915066
chr11502859503105E06915751
chr11534033534130E06946925
chr11534156534220E06947048
chr11449140449294E070-37814
chr11452027452531E070-34577
chr11452536452752E070-34356
chr11468203468961E070-18147
chr11533116533378E07046008
chr11451917451975E071-35133
chr11452027452531E071-34577
chr11468203468961E071-18147
chr11476501476590E071-10518
chr11476777476837E071-10271
chr11477085477135E071-9973
chr11477159477329E071-9779
chr11477457477585E071-9523
chr11478958479092E071-8016
chr11479158479332E071-7776
chr11479455479574E071-7534
chr11493906494047E0716798
chr11494058494130E0716950
chr11494241494313E0717133
chr11494370494468E0717262
chr11494512494631E0717404
chr11494697495232E0717589
chr11495269495499E0718161
chr11495547495630E0718439
chr11495663496075E0718555
chr11496162496265E0719054
chr11496298496347E0719190
chr11500023500103E07112915
chr11500150500204E07113042
chr11500300500354E07113192
chr11500379500437E07113271
chr11500499500850E07113391
chr11501049501247E07113941
chr11501292501441E07114184
chr11501478501825E07114370
chr11501848501898E07114740
chr11502035502126E07114927
chr11502174502387E07115066
chr11502859503105E07115751
chr11533451533607E07146343
chr11533791534008E07146683
chr11534033534130E07146925
chr11534156534220E07147048
chr11449140449294E072-37814
chr11451917451975E072-35133
chr11452027452531E072-34577
chr11452536452752E072-34356
chr11468203468961E072-18147
chr11468994469034E072-18074
chr11469139469267E072-17841
chr11472227472287E072-14821
chr11472344472499E072-14609
chr11476189476245E072-10863
chr11476501476590E072-10518
chr11476777476837E072-10271
chr11477085477135E072-9973
chr11477159477329E072-9779
chr11477457477585E072-9523
chr11477755477862E072-9246
chr11478958479092E072-8016
chr11479158479332E072-7776
chr11479455479574E072-7534
chr11483789483839E072-3269
chr11488166488295E0721058
chr11488364488445E0721256
chr11488497488547E0721389
chr11488609488670E0721501
chr11489126489403E0722018
chr11489467489517E0722359
chr11489720489770E0722612
chr11490602490804E0723494
chr11490808490965E0723700
chr11491061491286E0723953
chr11493906494047E0726798
chr11494058494130E0726950
chr11494241494313E0727133
chr11494370494468E0727262
chr11494512494631E0727404
chr11494697495232E0727589
chr11495269495499E0728161
chr11495547495630E0728439
chr11495663496075E0728555
chr11496162496265E0729054
chr11496298496347E0729190
chr11496501496598E0729393
chr11496751497301E0729643
chr11497354497462E07210246
chr11497599498241E07210491
chr11498278498426E07211170
chr11498451498524E07211343
chr11498529498628E07211421
chr11498693499250E07211585
chr11499324499461E07212216
chr11499488499581E07212380
chr11501049501247E07213941
chr11501292501441E07214184
chr11501478501825E07214370
chr11501848501898E07214740
chr11502035502126E07214927
chr11502174502387E07215066
chr11502430502826E07215322
chr11502859503105E07215751
chr11533791534008E07246683
chr11534033534130E07246925
chr11534156534220E07247048
chr11476777476837E073-10271
chr11477085477135E073-9973
chr11477159477329E073-9779
chr11477457477585E073-9523
chr11479158479332E073-7776
chr11479455479574E073-7534
chr11494370494468E0737262
chr11494512494631E0737404
chr11494697495232E0737589
chr11495269495499E0738161
chr11495547495630E0738439
chr11495663496075E0738555
chr11496162496265E0739054
chr11496298496347E0739190
chr11501478501825E07314370
chr11501848501898E07314740
chr11502035502126E07314927
chr11502174502387E07315066
chr11502430502826E07315322
chr11502859503105E07315751
chr11533451533607E07346343
chr11533791534008E07346683
chr11449140449294E074-37814
chr11451917451975E074-35133
chr11468203468961E074-18147
chr11468994469034E074-18074
chr11469139469267E074-17841
chr11469367469461E074-17647
chr11476501476590E074-10518
chr11476777476837E074-10271
chr11477085477135E074-9973
chr11477159477329E074-9779
chr11477457477585E074-9523
chr11478958479092E074-8016
chr11479158479332E074-7776
chr11479455479574E074-7534
chr11493906494047E0746798
chr11494058494130E0746950
chr11494241494313E0747133
chr11494370494468E0747262
chr11494512494631E0747404
chr11494697495232E0747589
chr11495269495499E0748161
chr11495547495630E0748439
chr11495663496075E0748555
chr11496162496265E0749054
chr11496298496347E0749190
chr11499603499701E07412495
chr11499719499778E07412611
chr11499830499904E07412722
chr11500023500103E07412915
chr11500150500204E07413042
chr11500300500354E07413192
chr11500379500437E07413271
chr11500499500850E07413391
chr11501049501247E07413941
chr11501292501441E07414184
chr11501478501825E07414370
chr11501848501898E07414740
chr11502035502126E07414927
chr11502174502387E07415066
chr11502430502826E07415322
chr11502859503105E07415751
chr11534033534130E07446925
chr11534156534220E07447048
chr11449140449294E081-37814
chr11451917451975E081-35133
chr11452027452531E081-34577
chr11533116533378E08146008
chr11533451533607E08146343
chr11533791534008E08146683
chr11534033534130E08146925
chr11534156534220E08147048
chr11451917451975E082-35133
chr11452027452531E082-34577
chr11452536452752E082-34356










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11447922449037E067-38071
chr11449822451623E067-35485
chr11506103508291E06718995
chr11518423519269E06731315
chr11447922449037E068-38071
chr11449822451623E068-35485
chr11506103508291E06818995
chr11518423519269E06831315
chr11447922449037E069-38071
chr11449822451623E069-35485
chr11506103508291E06918995
chr11518423519269E06931315
chr11447922449037E070-38071
chr11449822451623E070-35485
chr11506103508291E07018995
chr11447922449037E071-38071
chr11449822451623E071-35485
chr11506103508291E07118995
chr11518423519269E07131315
chr11447922449037E072-38071
chr11449822451623E072-35485
chr11506103508291E07218995
chr11518423519269E07231315
chr11447922449037E073-38071
chr11449822451623E073-35485
chr11506103508291E07318995
chr11447922449037E074-38071
chr11449822451623E074-35485
chr11506103508291E07418995
chr11518423519269E07431315
chr11449822451623E081-35485
chr11506103508291E08118995
chr11447922449037E082-38071
chr11449822451623E082-35485
chr11506103508291E08218995
chr11518423519269E08231315