chr15:78888400:G>A Detail (hg19) (CHRNA3)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr15:78,888,400-78,888,400 |
| hg38 | chr15:78,596,058-78,596,058 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001166694.1:c.1390-2867C>T | |
| NM_000743.4:c.*546C>T | ||
| Ensemble | ENST00000348639.7:c.1390-2867C>T |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.856 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:[No Data.] |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.012 | Carcinoma of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| 0.179 | Malignant neoplasm of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| 0.060 | Malignant neoplasm of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| 0.010 | Carcinoma of lung | A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) ... | BeFree | 20587604 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| 0.133 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| 0.020 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| <0.001 | nicotine dependence | We investigated six variants known to influence nicotine addiction or alcohol me... | BeFree | 24505444 | Detail |
| 0.133 | nicotine dependence | Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968... | BeFree | 20840187 | Detail |
| 0.006 | nicotine dependence | Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968... | BeFree | 20840187 | Detail |
| <0.001 | nicotine dependence | Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968... | BeFree | 20840187 | Detail |
| 0.133 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| <0.001 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.020 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.060 | Malignant neoplasm of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.010 | Carcinoma of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.003 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.002 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| 0.012 | Carcinoma of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.179 | Malignant neoplasm of lung | Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CH... | BeFree | 21862624 | Detail |
| 0.001 | nicotine dependence | The purpose of this study was to analyse the association of smoking status and s... | BeFree | 22046326 | Detail |
| <0.001 | attention deficit hyperactivity disorder | Our results demonstrate that the minor alleles of two polymorphisms (rs578776 an... | BeFree | 24375168 | Detail |
| 0.133 | Alcoholic Intoxication, Chronic | We also observed two SNPs associated with alcohol dependence, that is, rs615470 ... | BeFree | 20485328 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| A four-SNP haplotype spanning CHRNA5 (rs11637635 C, rs17408276 T, rs16969968 G) and CHRNA3 (rs578776... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| We investigated six variants known to influence nicotine addiction or alcohol metabolism, including ... | DisGeNET | Detail |
| Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968), CHRNA3 (rs578776)... | DisGeNET | Detail |
| Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968), CHRNA3 (rs578776)... | DisGeNET | Detail |
| Here we test the hypothesis that the nicotinic receptor genes CHRNA5 (rs16969968), CHRNA3 (rs578776)... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| Two variants in the nicotinic acetylcholine receptor subunit genes CHRNA5 and CHRNA3 on 15q25, rs169... | DisGeNET | Detail |
| The purpose of this study was to analyse the association of smoking status and smoking-related pheno... | DisGeNET | Detail |
| Our results demonstrate that the minor alleles of two polymorphisms (rs578776 and rs3743078) in the ... | DisGeNET | Detail |
| We also observed two SNPs associated with alcohol dependence, that is, rs615470 in CHRNA5 (OR=0.77, ... | DisGeNET | Detail |
Overlapped Transcript Coordinates
| Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
|---|
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs578776 dbSNP
- Genome
- hg19
- Position
- chr15:78,888,400-78,888,400
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs578776
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.8562
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 14350
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
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