chr3:52224356:T>C Detail (hg38) (TLR9)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:52,258,372-52,258,372 View the variant detail on this assembly version. |
| hg38 | chr3:52,224,356-52,224,356 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_017442.3:c.4-44A>G | |
| Ensemble | ENST00000360658.3:c.4-44A>G |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.508 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.370 |
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 |
|---|---|---|---|---|---|
| <0.001 | Acute GVH disease | We found that two tagSNPs in the TLR9 gene in the donor side, +1174 A/G (rs35213... | BeFree | 24121213 | Detail |
| 0.009 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.033 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.008 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.005 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.010 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.003 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.098 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.012 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.183 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.422 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.003 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.131 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| <0.001 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.008 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.004 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| <0.001 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.034 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.144 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| <0.001 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.008 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.130 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.187 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.012 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.004 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.131 | ulcerative colitis | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| <0.001 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.009 | Crohn Disease | Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory resp... | BeFree | 24776844 | Detail |
| 0.012 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.008 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.183 | Crohn Disease | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.009 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.013 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.009 | Crohn Disease | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| <0.001 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.327 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.001 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.009 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.131 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.126 | Crohn Disease | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.295 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.034 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| <0.001 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
| 0.187 | ulcerative colitis | The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL... | BeFree | 24971461 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| We found that two tagSNPs in the TLR9 gene in the donor side, +1174 A/G (rs352139) and +1635 C/T (rs... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| Nineteen functional polymorphisms that alter the NFκB-mediated inflammatory response (TLR2 (rs380409... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
| The polymorphisms TLR2 (rs1816702), NFKB1 (rs28362491), TNFRSF1A (rs4149570), IL6R (rs4537545), IL23... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs352139 dbSNP
- Genome
- hg38
- Position
- chr3:52,224,356-52,224,356
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- 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))
- rs352139
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.5078
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8509
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16758
- East Asian Chromosome Counts (ExAC)
- 690
- East Asian Allele Counts (ExAC)
- 255
- East Asian Heterozygous Counts (ExAC)
- 173
- East Asian Homozygous Counts (ExAC)
- 41
- East Asian Allele Frequency (ExAC)
- 0.3695652173913043
- Chromosome Counts in All Race (ExAC)
- 19456
- Allele Counts in All Race (ExAC)
- 10022
- Heterozygous Counts in All Race (ExAC)
- 4834
- Homozygous Counts in All Race (ExAC)
- 2594
- Allele Frequency in All Race (ExAC)
- 0.5151110197368421
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