rs11604385

Homo sapiens
C>T
SHANK2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0195 (5862/29916,GnomAD)
T=0166 (4844/29118,TOPMED)
T=0156 (781/5008,1000G)
T=0256 (987/3854,ALSPAC)
T=0250 (926/3708,TWINSUK)
chr11:70574867 (GRCh38.p7) (11q13.4)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.70574867C>T
GRCh37.p13 chr 11 fix patch HG865_PATCHNW_004070871.1:g.119080C>T
GRCh37.p13 chr 11NC_000011.9:g.70420972C>T

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/AIntron Variant
SHANK2 transcript variant 3NR_110766.1:n.N/AIntron 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
1000GenomesAfricanSub1322C=0.942T=0.058
1000GenomesAmericanSub694C=0.870T=0.130
1000GenomesEast AsianSub1008C=0.955T=0.045
1000GenomesEuropeSub1006C=0.741T=0.259
1000GenomesGlobalStudy-wide5008C=0.844T=0.156
1000GenomesSouth AsianSub978C=0.680T=0.320
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.744T=0.256
The Genome Aggregation DatabaseAfricanSub8710C=0.918T=0.082
The Genome Aggregation DatabaseAmericanSub834C=0.840T=0.160
The Genome Aggregation DatabaseEast AsianSub1622C=0.967T=0.033
The Genome Aggregation DatabaseEuropeSub18448C=0.734T=0.266
The Genome Aggregation DatabaseGlobalStudy-wide29916C=0.804T=0.195
The Genome Aggregation DatabaseOtherSub302C=0.790T=0.210
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.833T=0.166
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.750T=0.250
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
rs116043850.00092alcohol dependence20201924

eQTL of rs11604385 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 rs11604385 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.