rs7626587
Homo sapiens
A>G
CLSTN2 : Intron Variant
SNV (Single Nucleotide Variation)
A==0093 (2784/29930,GnomAD)
A==0126 (3689/29118,TOPMED)
A==0111 (557/5008,1000G)
A==0038 (146/3854,ALSPAC)
A==0035 (131/3708,TWINSUK)
A==0126 (3689/29118,TOPMED)
A==0111 (557/5008,1000G)
A==0038 (146/3854,ALSPAC)
A==0035 (131/3708,TWINSUK)
chr3:140274852 (GRCh38.p7) (3q23)
AD
GWASdb2
Genomic Coordinates
| Sequence Name | Change(s) |
|---|---|
| GRCh38.p7 chr 3 | NC_000003.12:g.140274852A>G |
| GRCh37.p13 chr 3 | NC_000003.11:g.139993694A>G |
Gene: CLSTN2, calsyntenin 2(plus strand)
| Molecule type | Change | Amino acid[Codon] | SO Term |
|---|---|---|---|
| CLSTN2 transcript | NM_022131.2:c. | N/A | Intron Variant |
| CLSTN2 transcript variant X1 | XM_017007022.1:c. | N/A | Intron Variant |
Population Frequency
| Study | Population | Group | Sample # | Ref Allele | Alt Allele |
|---|---|---|---|---|---|
| 1000Genomes | African | Sub | 1322 | A=0.239 | G=0.761 |
| 1000Genomes | American | Sub | 694 | A=0.040 | G=0.960 |
| 1000Genomes | East Asian | Sub | 1008 | A=0.028 | G=0.972 |
| 1000Genomes | Europe | Sub | 1006 | A=0.041 | G=0.959 |
| 1000Genomes | Global | Study-wide | 5008 | A=0.111 | G=0.889 |
| 1000Genomes | South Asian | Sub | 978 | A=0.150 | G=0.850 |
| The Avon Longitudinal Study of Parents and Children | PARENT AND CHILD COHORT | Study-wide | 3854 | A=0.038 | G=0.962 |
| The Genome Aggregation Database | African | Sub | 8700 | A=0.224 | G=0.776 |
| The Genome Aggregation Database | American | Sub | 838 | A=0.020 | G=0.980 |
| The Genome Aggregation Database | East Asian | Sub | 1612 | A=0.036 | G=0.964 |
| The Genome Aggregation Database | Europe | Sub | 18478 | A=0.039 | G=0.960 |
| The Genome Aggregation Database | Global | Study-wide | 29930 | A=0.093 | G=0.907 |
| The Genome Aggregation Database | Other | Sub | 302 | A=0.060 | G=0.940 |
| Trans-Omics for Precision Medicine | Global | Study-wide | 29118 | A=0.126 | G=0.873 |
| UK 10K study - Twins | TWIN COHORT | Study-wide | 3708 | A=0.035 | G=0.965 |
| PMID | Title | Author | Journal |
|---|---|---|---|
| 20201924 | Genome-wide association study of alcohol dependence implicates a region on chromosome 11. | Edenberg HJ | Alcohol Clin Exp Res |
P-Value
| SNP ID | p-value | Traits | Study |
|---|---|---|---|
| rs7626587 | 0.000808 | alcohol dependence | 20201924 |
eQTL of rs7626587 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 rs7626587 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 ) |
|---|---|---|---|---|
| chr3 | 139967989 | 139968043 | E068 | -25651 |
| chr3 | 139968084 | 139968314 | E068 | -25380 |
| chr3 | 139957663 | 139957728 | E069 | -35966 |
| chr3 | 139969769 | 139970083 | E071 | -23611 |
| chr3 | 139957663 | 139957728 | E072 | -35966 |
| chr3 | 139967989 | 139968043 | E072 | -25651 |
| chr3 | 139968084 | 139968314 | E072 | -25380 |
| chr3 | 140018762 | 140018954 | E081 | 25068 |
| chr3 | 140034136 | 140034296 | E081 | 40442 |
| chr3 | 140034873 | 140035408 | E081 | 41179 |
| chr3 | 140018762 | 140018954 | E082 | 25068 |
| chr3 | 140034873 | 140035408 | E082 | 41179 |