chr6:33033022:A>G Detail (hg19) (HLA-DPA1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:33,033,022-33,033,022 |
| hg38 | chr6:33,065,245-33,065,245 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001242524.1:c.*115T>C | |
| NM_001242525.1:c.*115T>C | ||
| NM_033554.3:c.*115T>C |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | |
| GWAS entry | 372 |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.610 | |
| 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
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
not provided
|
hepatitis B |
MGS000002
(TMGS000002) |
Masashi Mizokami | National Center for Global Health and Medicine | |||||
|
not provided
|
biliary cirrhosis, primary |
not provided
|
MGS000089
(TMGS000168) |
Minoru Nakamura Minoru Nakamura |
National Hospital Organization Nagasaki Medical Center National Hospital Organization Nagasaki Medical Center |
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.009 | hepatitis B | This was a retrospective cohort study.We genotyped seven SNPs in the following g... | BeFree | 25376093 | Detail |
| 0.011 | hepatitis B | This was a retrospective cohort study.We genotyped seven SNPs in the following g... | BeFree | 25376093 | Detail |
| 0.248 | Hepatitis B, Chronic | Genetic variants in five novel loci including CFB and CD40 predispose to chronic... | GWASCAT | 25802187 | Detail |
| <0.001 | Persistent infection | In addition, HLA-DP rs3077 showed an approaching significant effect on susceptib... | BeFree | 22105689 | Detail |
| 0.251 | Hepatitis B, Chronic | Chronic hepatitis B susceptibility loci in HLA-DP region (rs3077 and rs9277535) ... | BeFree | 21408128 | Detail |
| 0.132 | hepatitis B | Two single nucleotide polymorphisms (SNP), rs3077 near HLA-DPA1 region and rs927... | BeFree | 23326374 | Detail |
| 0.132 | hepatitis B | In addition, Uygurs have higher frequencies of HLA-DP/DQ protective alleles (72.... | BeFree | 25041342 | Detail |
| 0.248 | Hepatitis B, Chronic | [A genome-wide association study of chronic hepatitis B identified novel risk lo... | GAD | 21750111 | Detail |
| 0.123 | hepatitis B | We genotyped SNPs rs3077 (near HLA-DPA1) and rs9277378 and rs3128917 (both near ... | BeFree | 23825586 | Detail |
| 0.132 | hepatitis B | Association of the rs3077 and rs9277535 polymorphisms in HLA-DP with hepatitis B... | BeFree | 23601003 | Detail |
| 0.123 | hepatitis B | Genome-wide association study confirming association of HLA-DP with protection a... | GWASCAT | 22737229 | Detail |
| 0.248 | Hepatitis B, Chronic | A genome-wide association study identified new variants associated with the risk... | GWASCAT | 23760081 | Detail |
| 0.001 | Hepatitis B, Chronic | A genome-wide association study identified single nucleotide polymorphisms (SNPs... | BeFree | 21346778 | Detail |
| 0.004 | liver carcinoma | HLA-DP/DQ polymorphisms (rs3077, rs9277535, rs7453920) did not associate with HC... | BeFree | 25365208 | Detail |
| 0.123 | hepatitis B | Two single nucleotide polymorphisms (SNP), rs3077 near HLA-DPA1 region and rs927... | BeFree | 23326374 | Detail |
| 0.123 | hepatitis B | Japanese patients (202) who were hepatitis B e antigen positive at baseline, rec... | BeFree | 25103089 | Detail |
| 0.123 | hepatitis B | A genome-wide association study of chronic hepatitis B identified novel risk loc... | GWASCAT | 21750111 | Detail |
| 0.248 | Hepatitis B, Chronic | We also found that the HLA-DPA1 and HLA-DPB1 genes were significantly associated... | BeFree | 22737229 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| This was a retrospective cohort study.We genotyped seven SNPs in the following genes, interleukin (I... | DisGeNET | Detail |
| This was a retrospective cohort study.We genotyped seven SNPs in the following genes, interleukin (I... | DisGeNET | Detail |
| Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B. | DisGeNET | Detail |
| In addition, HLA-DP rs3077 showed an approaching significant effect on susceptibility to HBV persist... | DisGeNET | Detail |
| Chronic hepatitis B susceptibility loci in HLA-DP region (rs3077 and rs9277535) identified by genome... | DisGeNET | Detail |
| Two single nucleotide polymorphisms (SNP), rs3077 near HLA-DPA1 region and rs9277535 near HLA-DPB1 r... | DisGeNET | Detail |
| In addition, Uygurs have higher frequencies of HLA-DP/DQ protective alleles (72.5% for rs3077, 76.6%... | DisGeNET | Detail |
| [A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese po... | DisGeNET | Detail |
| We genotyped SNPs rs3077 (near HLA-DPA1) and rs9277378 and rs3128917 (both near HLA-DPB1) in 500 HBV... | DisGeNET | Detail |
| Association of the rs3077 and rs9277535 polymorphisms in HLA-DP with hepatitis B virus infection and... | DisGeNET | Detail |
| Genome-wide association study confirming association of HLA-DP with protection against chronic hepat... | DisGeNET | Detail |
| A genome-wide association study identified new variants associated with the risk of chronic hepatiti... | DisGeNET | Detail |
| A genome-wide association study identified single nucleotide polymorphisms (SNPs) rs3077 and rs92775... | DisGeNET | Detail |
| HLA-DP/DQ polymorphisms (rs3077, rs9277535, rs7453920) did not associate with HCC development, but d... | DisGeNET | Detail |
| Two single nucleotide polymorphisms (SNP), rs3077 near HLA-DPA1 region and rs9277535 near HLA-DPB1 r... | DisGeNET | Detail |
| Japanese patients (202) who were hepatitis B e antigen positive at baseline, received LAM as first-l... | DisGeNET | Detail |
| A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese pop... | DisGeNET | Detail |
| We also found that the HLA-DPA1 and HLA-DPB1 genes were significantly associated with protective eff... | 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
- rs3077 dbSNP
- Genome
- hg19
- Position
- chr6:33,033,022-33,033,022
- 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))
- rs3077
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.6104
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 10231
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
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