rs7940843

Homo sapiens
T>C
SHANK2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0418 (12523/29910,GnomAD)
T==0399 (11634/29118,TOPMED)
C=0494 (2475/5008,1000G)
T==0368 (1418/3854,ALSPAC)
T==0360 (1334/3708,TWINSUK)
chr11:70680240 (GRCh38.p7) (11q13.4)
AD
GWASdb2
1   publication(s)
See rs on genome
97 Enhancers around
20 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.70680240T>C
GRCh37.p13 chr 11 fix patch HG865_PATCHNW_004070871.1:g.224453T>C
GRCh37.p13 chr 11NC_000011.9:g.70526345T>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 X4XM_005277932.3:c.N/AIntron 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 X5XM_017017390.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.445C=0.555
1000GenomesAmericanSub694T=0.520C=0.480
1000GenomesEast AsianSub1008T=0.693C=0.307
1000GenomesEuropeSub1006T=0.354C=0.646
1000GenomesGlobalStudy-wide5008T=0.506C=0.494
1000GenomesSouth AsianSub978T=0.540C=0.460
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.368C=0.632
The Genome Aggregation DatabaseAfricanSub8706T=0.425C=0.575
The Genome Aggregation DatabaseAmericanSub836T=0.480C=0.520
The Genome Aggregation DatabaseEast AsianSub1616T=0.689C=0.311
The Genome Aggregation DatabaseEuropeSub18450T=0.388C=0.611
The Genome Aggregation DatabaseGlobalStudy-wide29910T=0.418C=0.581
The Genome Aggregation DatabaseOtherSub302T=0.440C=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.399C=0.600
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.360C=0.640
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
rs79408434.1E-05alcoholism (heaviness of drinking)21529783

eQTL of rs7940843 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 rs7940843 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 )
chr11194776194844E067-29609
chr11205254205333E067-19120
chr11209905210484E067-13969
chr11210495210619E067-13834
chr11210648210716E067-13737
chr11210723210819E067-13634
chr11210912211003E067-13450
chr11211026211076E067-13377
chr11211153211287E067-13166
chr11211364211459E067-12994
chr11211463211539E067-12914
chr11211635211695E067-12758
chr11211782211888E067-12565
chr11212043212105E067-12348
chr11228240228334E0683787
chr11235188235238E06810735
chr11190398190993E069-33460
chr11210495210619E069-13834
chr11210648210716E069-13737
chr11210723210819E069-13634
chr11210912211003E069-13450
chr11211026211076E069-13377
chr11211153211287E069-13166
chr11211364211459E069-12994
chr11211463211539E069-12914
chr11238453238521E06914000
chr11204829204931E070-19522
chr11205052205196E070-19257
chr11205254205333E070-19120
chr11210723210819E070-13634
chr11210912211003E070-13450
chr11211026211076E070-13377
chr11211153211287E070-13166
chr11211364211459E070-12994
chr11211463211539E070-12914
chr11211635211695E070-12758
chr11211782211888E070-12565
chr11215286215389E070-9064
chr11215524215682E070-8771
chr11234696234837E07010243
chr11238453238521E07014000
chr11238671238762E07014218
chr11238794238834E07014341
chr11209905210484E071-13969
chr11210495210619E071-13834
chr11210648210716E071-13737
chr11210723210819E071-13634
chr11210912211003E071-13450
chr11211026211076E071-13377
chr11211153211287E071-13166
chr11211364211459E071-12994
chr11235188235238E07110735
chr11194776194844E072-29609
chr11203726203810E072-20643
chr11203836204155E072-20298
chr11204206204260E072-20193
chr11204331204414E072-20039
chr11210495210619E072-13834
chr11210648210716E072-13737
chr11210723210819E072-13634
chr11210912211003E072-13450
chr11238453238521E07214000
chr11203402203583E073-20870
chr11203594203648E073-20805
chr11203726203810E073-20643
chr11203836204155E073-20298
chr11204206204260E073-20193
chr11204331204414E073-20039
chr11204562204754E073-19699
chr11204829204931E073-19522
chr11205052205196E073-19257
chr11205254205333E073-19120
chr11209905210484E073-13969
chr11210495210619E073-13834
chr11210648210716E073-13737
chr11210723210819E073-13634
chr11210912211003E073-13450
chr11211026211076E073-13377
chr11211153211287E073-13166
chr11211364211459E073-12994
chr11235188235238E07310735
chr11238453238521E07314000
chr11204829204931E074-19522
chr11205052205196E074-19257
chr11205254205333E074-19120
chr11209905210484E074-13969
chr11209905210484E081-13969
chr11210495210619E081-13834
chr11210648210716E081-13737
chr11210723210819E081-13634
chr11210912211003E081-13450
chr11211026211076E081-13377
chr11211153211287E081-13166
chr11211364211459E081-12994
chr11234696234837E08110243
chr11235188235238E08110735
chr11238453238521E08114000









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11205371209902E067-14551
chr11235291237738E06710838
chr11205371209902E068-14551
chr11235291237738E06810838
chr11205371209902E069-14551
chr11235291237738E06910838
chr11205371209902E070-14551
chr11235291237738E07010838
chr11205371209902E071-14551
chr11235291237738E07110838
chr11205371209902E072-14551
chr11235291237738E07210838
chr11205371209902E073-14551
chr11235291237738E07310838
chr11205371209902E074-14551
chr11235291237738E07410838
chr11205371209902E081-14551
chr11235291237738E08110838
chr11205371209902E082-14551
chr11235291237738E08210838