rs3924047

Homo sapiens
T>C
SHANK2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0493 (14761/29894,GnomAD)
C=0482 (14059/29118,TOPMED)
T==0474 (6772/14288,ExAC)
T==0481 (2407/5008,1000G)
T==0477 (2179/4566,GO-ESP)
C=0495 (1907/3854,ALSPAC)
C=0481 (1784/3708,TWINSUK)
chr11:71118812 (GRCh38.p7) (11q13.4)
AD
GWASdb2
2   publication(s)
See rs on genome
109 Enhancers around
38 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.71118812T>C
GRCh37.p13 chr 11 fix patch HG865_PATCHNW_004070871.1:g.613025T>C
GRCh37.p13 chr 11NC_000011.9:g.70829858T>C

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
1000GenomesAfricanSub1322T=0.482C=0.518
1000GenomesAmericanSub694T=0.440C=0.560
1000GenomesEast AsianSub1008T=0.384C=0.616
1000GenomesEuropeSub1006T=0.500C=0.500
1000GenomesGlobalStudy-wide5008T=0.481C=0.519
1000GenomesSouth AsianSub978T=0.580C=0.420
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.505C=0.495
The Exome Aggregation ConsortiumAmericanSub2428T=0.500C=0.500
The Exome Aggregation ConsortiumAsianSub3754T=0.446C=0.554
The Exome Aggregation ConsortiumEuropeSub7964T=0.479C=0.521
The Exome Aggregation ConsortiumGlobalStudy-wide14288T=0.474C=0.526
The Exome Aggregation ConsortiumOtherSub142T=0.450C=0.550
The Genome Aggregation DatabaseAfricanSub8706T=0.521C=0.479
The Genome Aggregation DatabaseAmericanSub834T=0.450C=0.550
The Genome Aggregation DatabaseEast AsianSub1612T=0.389C=0.611
The Genome Aggregation DatabaseEuropeSub18440T=0.510C=0.489
The Genome Aggregation DatabaseGlobalStudy-wide29894T=0.506C=0.493
The Genome Aggregation DatabaseOtherSub302T=0.600C=0.400
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.517C=0.482
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.519C=0.481
PMID Title Author Journal
16400611Genomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the combined sample.Suarez BKAm J Hum Genet
23691058Dosage transmission disequilibrium test (dTDT) for linkage and association detection.Zhang ZPLoS One

P-Value

SNP ID p-value Traits Study
rs39240478.77E-06alcohol dependence23691058

eQTL of rs3924047 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 rs3924047 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr11578622578923E067-34102
chr11579295579830E067-33195
chr11579896579951E067-33074
chr11580027580591E067-32434
chr11581922581972E067-31053
chr11632579632671E06719554
chr11632853633265E06719828
chr11571203572078E068-40947
chr11572115572210E068-40815
chr11578622578923E068-34102
chr11579058579102E068-33923
chr11579186579249E068-33776
chr11579295579830E068-33195
chr11579896579951E068-33074
chr11580027580591E068-32434
chr11581922581972E068-31053
chr11614155614458E0681130
chr11658284658350E06845259
chr11658432658924E06845407
chr11578622578923E069-34102
chr11579058579102E069-33923
chr11579186579249E069-33776
chr11579295579830E069-33195
chr11579896579951E069-33074
chr11580027580591E069-32434
chr11614155614458E0691130
chr11632579632671E06919554
chr11632853633265E06919828
chr11658284658350E06945259
chr11569960570100E070-42925
chr11570113570215E070-42810
chr11578622578923E070-34102
chr11579058579102E070-33923
chr11579186579249E070-33776
chr11579295579830E070-33195
chr11579896579951E070-33074
chr11580027580591E070-32434
chr11580655580709E070-32316
chr11614155614458E0701130
chr11578622578923E071-34102
chr11579058579102E071-33923
chr11579186579249E071-33776
chr11579295579830E071-33195
chr11579896579951E071-33074
chr11580027580591E071-32434
chr11585460585564E071-27461
chr11587478588405E071-24620
chr11614155614458E0711130
chr11628527628893E07115502
chr11629062629215E07116037
chr11632579632671E07119554
chr11632853633265E07119828
chr11658284658350E07145259
chr11658432658924E07145407
chr11573158573208E072-39817
chr11573276573473E072-39552
chr11573527573571E072-39454
chr11573577573647E072-39378
chr11573746573796E072-39229
chr11578622578923E072-34102
chr11579058579102E072-33923
chr11579186579249E072-33776
chr11579295579830E072-33195
chr11579896579951E072-33074
chr11606022606109E072-6916
chr11606130606170E072-6855
chr11606272606606E072-6419
chr11606695606803E072-6222
chr11614155614458E0721130
chr11632510632560E07219485
chr11632579632671E07219554
chr11632853633265E07219828
chr11658284658350E07245259
chr11658432658924E07245407
chr11578622578923E073-34102
chr11579058579102E073-33923
chr11579186579249E073-33776
chr11579295579830E073-33195
chr11579896579951E073-33074
chr11658432658924E07345407
chr11573158573208E074-39817
chr11573276573473E074-39552
chr11573527573571E074-39454
chr11573577573647E074-39378
chr11578622578923E074-34102
chr11579058579102E074-33923
chr11579186579249E074-33776
chr11579295579830E074-33195
chr11579896579951E074-33074
chr11580027580591E074-32434
chr11614155614458E0741130
chr11616501617304E0743476
chr11658284658350E07445259
chr11658432658924E07445407
chr11569960570100E081-42925
chr11570113570215E081-42810
chr11578622578923E081-34102
chr11579058579102E081-33923
chr11579186579249E081-33776
chr11579295579830E081-33195
chr11579896579951E081-33074
chr11580027580591E081-32434
chr11614155614458E0811130
chr11578622578923E082-34102
chr11579058579102E082-33923
chr11579186579249E082-33776
chr11579295579830E082-33195
chr11579896579951E082-33074
chr11614155614458E0821130










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11567281569927E067-43098
chr11574250576772E067-36253
chr11576899577749E067-35276
chr11614468616352E0671443
chr11567281569927E068-43098
chr11574250576772E068-36253
chr11576899577749E068-35276
chr11614468616352E0681443
chr11567281569927E069-43098
chr11574250576772E069-36253
chr11576899577749E069-35276
chr11567281569927E070-43098
chr11574250576772E070-36253
chr11576899577749E070-35276
chr11614468616352E0701443
chr11567281569927E071-43098
chr11574250576772E071-36253
chr11576899577749E071-35276
chr11614468616352E0711443
chr11567281569927E072-43098
chr11574250576772E072-36253
chr11576899577749E072-35276
chr11567281569927E073-43098
chr11574250576772E073-36253
chr11576899577749E073-35276
chr11614468616352E0731443
chr11567281569927E074-43098
chr11574250576772E074-36253
chr11576899577749E074-35276
chr11614468616352E0741443
chr11576899577749E081-35276
chr11567281569927E082-43098
chr11574250576772E082-36253
chr11576899577749E082-35276
chr11614468616352E0821443
chr11636787637366E08223762
chr11639624639981E08226599
chr11640123640340E08227098