chr3:52222681:C>T Detail (hg38) (TLR9)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:52,256,697-52,256,697 View the variant detail on this assembly version. |
| hg38 | chr3:52,222,681-52,222,681 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_017442.3:c.1635G>A | NP_059138.1:p.Pro545= |
| Ensemble | ENST00000360658.3:c.1635G>A | ENST00000360658.3:p.Pro545= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.498 |
| ToMMo:0.504 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.380 |
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 |
|---|---|---|---|---|---|
| 0.011 | HIV Infections | Association of single-nucleotide polymorphisms in TLR7 (Gln11Leu) and TLR9 (1635... | BeFree | 24747071 | Detail |
| 0.010 | HIV Infections | Association of single-nucleotide polymorphisms in TLR7 (Gln11Leu) and TLR9 (1635... | BeFree | 24747071 | Detail |
| <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 |
| 0.340 | Inflammatory Bowel Diseases | The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs3... | BeFree | 19455129 | Detail |
| 0.011 | HIV Infections | Infants with the TLR9 1635A (rs352140) variant were more likely to acquire HIV-1... | BeFree | 24037211 | Detail |
| 0.133 | Inflammatory Bowel Diseases | The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs3... | BeFree | 19455129 | Detail |
| 0.016 | HIV Infections | : To analyze the influence of single-nucleotide polymorphisms (SNPs) in TLR2 (18... | BeFree | 18769358 | Detail |
| 0.020 | ulcerative colitis | The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs3... | BeFree | 19455129 | Detail |
| 0.002 | hepatitis B | To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like recep... | BeFree | 25388852 | Detail |
| 0.002 | hepatitis B | To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like recep... | BeFree | 25388852 | Detail |
| 0.157 | Inflammatory Bowel Diseases | The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs3... | BeFree | 19455129 | Detail |
| 0.011 | HIV Infections | : TLR9 1635A/G SNP might have a role in HIV clinical disease progression. | BeFree | 18769358 | Detail |
| <0.001 | Inflammatory Bowel Diseases | The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs3... | BeFree | 19455129 | Detail |
| 0.011 | HIV Infections | TLR9 1635A/G was associated with reduced HIV-1 acquisition among HIV-seronegativ... | BeFree | 24325963 | Detail |
| 0.173 | Inflammatory Bowel Diseases | The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs3... | BeFree | 19455129 | Detail |
| 0.007 | ulcerative colitis | The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs3... | BeFree | 19455129 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| Association of single-nucleotide polymorphisms in TLR7 (Gln11Leu) and TLR9 (1635A/G) with a higher C... | DisGeNET | Detail |
| Association of single-nucleotide polymorphisms in TLR7 (Gln11Leu) and TLR9 (1635A/G) with a higher C... | DisGeNET | Detail |
| We found that two tagSNPs in the TLR9 gene in the donor side, +1174 A/G (rs352139) and +1635 C/T (rs... | DisGeNET | Detail |
| The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs352140=p.Pro545Pro) i... | DisGeNET | Detail |
| Infants with the TLR9 1635A (rs352140) variant were more likely to acquire HIV-1 by 1 month [hazard ... | DisGeNET | Detail |
| The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs352140=p.Pro545Pro) i... | DisGeNET | Detail |
| : To analyze the influence of single-nucleotide polymorphisms (SNPs) in TLR2 (1892A/C and 2258G/A), ... | DisGeNET | Detail |
| The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs352140=p.Pro545Pro) i... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like receptors (TLRs) 3 and 9 ... | DisGeNET | Detail |
| To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like receptors (TLRs) 3 and 9 ... | DisGeNET | Detail |
| The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs352140=p.Pro545Pro) i... | DisGeNET | Detail |
| : TLR9 1635A/G SNP might have a role in HIV clinical disease progression. | DisGeNET | Detail |
| The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs352140=p.Pro545Pro) i... | DisGeNET | Detail |
| TLR9 1635A/G was associated with reduced HIV-1 acquisition among HIV-seronegative controls with high... | DisGeNET | Detail |
| The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs352140=p.Pro545Pro) i... | DisGeNET | Detail |
| The single-nucleotide polymorphisms (SNPs) -1237T/C (rs5743836) and 2848A/G (rs352140=p.Pro545Pro) i... | 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
- -
- Genome
- hg38
- Position
- chr3:52,222,681-52,222,681
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 70.16
- Standard deviation of sample read depth (HGVD)
- 31.91
- Number of reference allele (HGVD)
- 1215
- Number of alternative allele (HGVD)
- 1205
- Allele Frequency (HGVD)
- 0.49793388429752067
- Gene Symbol (HGVD)
- TLR9
- 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))
- rs352140
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.5039
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8443
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16756
- East Asian Chromosome Counts (ExAC)
- 8594
- East Asian Allele Counts (ExAC)
- 3262
- East Asian Heterozygous Counts (ExAC)
- 2024
- East Asian Homozygous Counts (ExAC)
- 619
- East Asian Allele Frequency (ExAC)
- 0.3795671398650221
- Chromosome Counts in All Race (ExAC)
- 120872
- Allele Counts in All Race (ExAC)
- 59483
- Heterozygous Counts in All Race (ExAC)
- 29429
- Homozygous Counts in All Race (ExAC)
- 15027
- Allele Frequency in All Race (ExAC)
- 0.49211562644781254
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