rs4077501

Homo sapiens
T>C
CLSTN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0044 (1335/29932,GnomAD)
T==0064 (1875/29118,TOPMED)
T==0062 (310/5008,1000G)
T==0014 (54/3854,ALSPAC)
T==0010 (37/3708,TWINSUK)
chr3:140278306 (GRCh38.p7) (3q23)
AD
GWASdb2
1   publication(s)
See rs on genome
12 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.140278306T>C
GRCh37.p13 chr 3NC_000003.11:g.139997148T>C

Gene: CLSTN2, calsyntenin 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CLSTN2 transcriptNM_022131.2:c.N/AIntron Variant
CLSTN2 transcript variant X1XM_017007022.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.132C=0.868
1000GenomesAmericanSub694T=0.010C=0.990
1000GenomesEast AsianSub1008T=0.028C=0.972
1000GenomesEuropeSub1006T=0.010C=0.990
1000GenomesGlobalStudy-wide5008T=0.062C=0.938
1000GenomesSouth AsianSub978T=0.090C=0.910
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.014C=0.986
The Genome Aggregation DatabaseAfricanSub8706T=0.119C=0.881
The Genome Aggregation DatabaseAmericanSub836T=0.010C=0.990
The Genome Aggregation DatabaseEast AsianSub1600T=0.033C=0.967
The Genome Aggregation DatabaseEuropeSub18488T=0.012C=0.987
The Genome Aggregation DatabaseGlobalStudy-wide29932T=0.044C=0.955
The Genome Aggregation DatabaseOtherSub302T=0.030C=0.970
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.064C=0.935
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.010C=0.990
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
rs40775010.000153alcohol dependence20201924

eQTL of rs4077501 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 rs4077501 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 )
chr3139967989139968043E068-29105
chr3139968084139968314E068-28834
chr3139957663139957728E069-39420
chr3139969769139970083E071-27065
chr3139957663139957728E072-39420
chr3139967989139968043E072-29105
chr3139968084139968314E072-28834
chr3140018762140018954E08121614
chr3140034136140034296E08136988
chr3140034873140035408E08137725
chr3140018762140018954E08221614
chr3140034873140035408E08237725