chr19:45395619:A>G Detail (hg19) (TOMM40)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr19:45,395,619-45,395,619 |
| hg38 | chr19:44,892,362-44,892,362 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001128917.1:c.275-31A>G | |
| NM_006114.2:c.275-31A>G | ||
| NM_001128916.1:c.275-31A>G |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | |
| GWAS entry | 3,738 |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.168 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.087 |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
Alzheimer disease |
not provided
|
MGS000015
(TMGS000120) |
Hiroshi Mori | Osaka City University | ||||
|
not provided
|
mild cognitive impairment |
not provided
|
MGS000015
(TMGS000120) |
Hiroshi Mori | Osaka City University |
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.440 | Alzheimer's disease | There were four significant associations between genotypes and phenotypes of AD ... | BeFree | 24530172 | Detail |
| 0.249 | Alzheimer's disease | There were four significant associations between genotypes and phenotypes of AD ... | BeFree | 24530172 | Detail |
| 0.159 | Alzheimer's disease | [In addition to known candidate genes, APOE, TOMM40, and one hypothetical gene L... | GAD | 21123754 | Detail |
| <0.001 | obesity | (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125... | BeFree | 24788522 | Detail |
| <0.001 | obesity | (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125... | BeFree | 24788522 | Detail |
| <0.001 | obesity | (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125... | BeFree | 24788522 | Detail |
| 0.196 | obesity | (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125... | BeFree | 24788522 | Detail |
| 0.159 | Alzheimer's disease | Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease pro... | GWASCAT | 20885792 | Detail |
| <0.001 | Unipolar Depression | TOMM40 rs2075650 may represent a new candidate gene for vulnerability to major d... | BeFree | 24549102 | Detail |
| 0.120 | Impaired cognition | A genome-wide association study implicates the APOE locus in nonpathological cog... | GWASCAT | 23207651 | Detail |
| 0.195 | age related macular degeneration | GWAS meta-analysis confirmed previously reported association of variants at the ... | BeFree | 23326517 | Detail |
| 0.159 | Alzheimer's disease | Here, we performed a meta-analysis combining data of 4,569 individuals (2,540 ca... | GWASCAT | 24755620 | Detail |
| 0.120 | Mental deterioration | A genome-wide association study implicates the APOE locus in nonpathological cog... | GWASCAT | 23207651 | Detail |
| 0.404 | age related macular degeneration | GWAS meta-analysis confirmed previously reported association of variants at the ... | BeFree | 23326517 | Detail |
| 0.121 | age related macular degeneration | Genome-wide association study of age-related macular degeneration identifies ass... | GWASCAT | 22694956 | Detail |
| 0.121 | age related macular degeneration | No evidence of association between variant rs2075650 in lipid metabolism-related... | BeFree | 25304313 | Detail |
| 0.159 | Alzheimer's disease | [Two genetic loci for AD were found for the first time to reach genome-wide stat... | GAD | 20460622 | Detail |
| 0.120 | Impaired cognition | The incident case study comparing patients who developed AD during longitudinal ... | BeFree | 24176626 | Detail |
| 0.121 | age related macular degeneration | Our data provide no evidence to support an association of rs2075650 in TOMM40 wi... | BeFree | 24146538 | Detail |
| 0.159 | Alzheimer's disease | Genome-wide association study identifies variants at CLU and CR1 associated with... | GWASCAT | 19734903 | Detail |
| 0.159 | Alzheimer's disease | [, we observed and replicated a novel statistically significant association in M... | GAD | 20885792 | Detail |
| <0.001 | Impaired cognition | Our prevalent case study comparing prevalent AD cases (n = 428) with participant... | BeFree | 24176626 | Detail |
| 0.159 | Alzheimer's disease | Recently, the rs2075650 single nucleotide polymorphism in the translocase of out... | BeFree | 24146538 | Detail |
| 0.121 | age related macular degeneration | Insights into the genetic architecture of early stage age-related macular degene... | GWASCAT | 23326517 | Detail |
| 0.200 | Impaired cognition | Our prevalent case study comparing prevalent AD cases (n = 428) with participant... | BeFree | 24176626 | Detail |
| 0.195 | age related macular degeneration | No evidence of association between variant rs2075650 in lipid metabolism-related... | BeFree | 25304313 | Detail |
| 0.138 | Carotid Artery Diseases | We found that two loci, chromosome 1p13.3 near CELSR2 and PSRC1 which contains r... | BeFree | 19951432 | Detail |
| <0.001 | Mental Depression | Our results suggest that TOMM40 rs2075650 may be a risk factor for the developme... | BeFree | 24549102 | Detail |
| 0.159 | Alzheimer's disease | Genome-wide analysis of genetic loci associated with Alzheimer disease. | GWASCAT | 20460622 | Detail |
| 0.159 | Alzheimer's disease | Genome-wide association study identifies variants at CLU and PICALM associated w... | GWASCAT | 19734902 | Detail |
| 0.159 | Alzheimer's disease | Genome-wide scan of copy number variation in late-onset Alzheimer's disease. | GWASCAT | 20061627 | Detail |
| <0.001 | depressive disorder | Our results suggest that TOMM40 rs2075650 may be a risk factor for the developme... | BeFree | 24549102 | Detail |
| <0.001 | major depressive disorder | TOMM40 rs2075650 may represent a new candidate gene for vulnerability to major d... | BeFree | 24549102 | Detail |
| 0.159 | Alzheimer's disease | [Genome-wide scan of copy number variation in late-onset Alzheimer\'s disease.] | GAD | 20061627 | Detail |
| <0.001 | Impaired cognition | The incident case study comparing patients who developed AD during longitudinal ... | BeFree | 24176626 | Detail |
| 0.159 | Alzheimer's disease | ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathol... | GWASCAT | 24770881 | Detail |
| 0.125 | Cardiovascular Diseases | Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with... | GWASCAT | 21943158 | Detail |
| 0.480 | age related macular degeneration | GWAS meta-analysis confirmed previously reported association of variants at the ... | GWASCAT | 23326517 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| There were four significant associations between genotypes and phenotypes of AD patients: CR1 SNP rs... | DisGeNET | Detail |
| There were four significant associations between genotypes and phenotypes of AD patients: CR1 SNP rs... | DisGeNET | Detail |
| [In addition to known candidate genes, APOE, TOMM40, and one hypothetical gene LOC100129500 partiall... | DisGeNET | Detail |
| (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125944 at FERMT2, pBMI ... | DisGeNET | Detail |
| (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125944 at FERMT2, pBMI ... | DisGeNET | Detail |
| (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125944 at FERMT2, pBMI ... | DisGeNET | Detail |
| (2) Four additional AD risk SNPs were nominally associated with obesity (rs17125944 at FERMT2, pBMI ... | DisGeNET | Detail |
| Dementia revealed: novel chromosome 6 locus for late-onset Alzheimer disease provides genetic eviden... | DisGeNET | Detail |
| TOMM40 rs2075650 may represent a new candidate gene for vulnerability to major depressive disorder. | DisGeNET | Detail |
| A genome-wide association study implicates the APOE locus in nonpathological cognitive ageing. | DisGeNET | Detail |
| GWAS meta-analysis confirmed previously reported association of variants at the complement factor H ... | DisGeNET | Detail |
| Here, we performed a meta-analysis combining data of 4,569 individuals (2,540 cases and 2,029 health... | DisGeNET | Detail |
| A genome-wide association study implicates the APOE locus in nonpathological cognitive ageing. | DisGeNET | Detail |
| GWAS meta-analysis confirmed previously reported association of variants at the complement factor H ... | DisGeNET | Detail |
| Genome-wide association study of age-related macular degeneration identifies associated variants in ... | DisGeNET | Detail |
| No evidence of association between variant rs2075650 in lipid metabolism-related locus APOE/TOMM40 a... | DisGeNET | Detail |
| [Two genetic loci for AD were found for the first time to reach genome-wide statistical significance... | DisGeNET | Detail |
| The incident case study comparing patients who developed AD during longitudinal observation (n = 152... | DisGeNET | Detail |
| Our data provide no evidence to support an association of rs2075650 in TOMM40 with nAMD or PCV, sugg... | DisGeNET | Detail |
| Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease... | DisGeNET | Detail |
| [, we observed and replicated a novel statistically significant association in MTHFD1L, a gene invol... | DisGeNET | Detail |
| Our prevalent case study comparing prevalent AD cases (n = 428) with participants with no cognitive ... | DisGeNET | Detail |
| Recently, the rs2075650 single nucleotide polymorphism in the translocase of outer mitochondrial mem... | DisGeNET | Detail |
| Insights into the genetic architecture of early stage age-related macular degeneration: a genome-wid... | DisGeNET | Detail |
| Our prevalent case study comparing prevalent AD cases (n = 428) with participants with no cognitive ... | DisGeNET | Detail |
| No evidence of association between variant rs2075650 in lipid metabolism-related locus APOE/TOMM40 a... | DisGeNET | Detail |
| We found that two loci, chromosome 1p13.3 near CELSR2 and PSRC1 which contains rs646776, and 19q13.2... | DisGeNET | Detail |
| Our results suggest that TOMM40 rs2075650 may be a risk factor for the development of depression cha... | DisGeNET | Detail |
| Genome-wide analysis of genetic loci associated with Alzheimer disease. | DisGeNET | Detail |
| Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's dise... | DisGeNET | Detail |
| Genome-wide scan of copy number variation in late-onset Alzheimer's disease. | DisGeNET | Detail |
| Our results suggest that TOMM40 rs2075650 may be a risk factor for the development of depression cha... | DisGeNET | Detail |
| TOMM40 rs2075650 may represent a new candidate gene for vulnerability to major depressive disorder. | DisGeNET | Detail |
| [Genome-wide scan of copy number variation in late-onset Alzheimer\'s disease.] | DisGeNET | Detail |
| The incident case study comparing patients who developed AD during longitudinal observation (n = 152... | DisGeNET | Detail |
| ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathology. | DisGeNET | Detail |
| Genetic variants in LPL, OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovasc... | DisGeNET | Detail |
| GWAS meta-analysis confirmed previously reported association of variants at the complement factor H ... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs2075650 dbSNP
- Genome
- hg19
- Position
- chr19:45,395,619-45,395,619
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- 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))
- rs2075650
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1675
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 2808
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8648
- East Asian Allele Counts (ExAC)
- 752
- East Asian Heterozygous Counts (ExAC)
- 690
- East Asian Homozygous Counts (ExAC)
- 31
- East Asian Allele Frequency (ExAC)
- 0.08695652173913043
- Chromosome Counts in All Race (ExAC)
- 121382
- Allele Counts in All Race (ExAC)
- 15709
- Heterozygous Counts in All Race (ExAC)
- 13631
- Homozygous Counts in All Race (ExAC)
- 1039
- Allele Frequency in All Race (ExAC)
- 0.1294178708539981
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