chr10:122461028:G>A Detail (hg38) (HTRA1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr10:124,220,544-124,220,544 View the variant detail on this assembly version. |
| hg38 | chr10:122,461,028-122,461,028 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | ||
| Ensemble | ENST00000648167.1:c.154+2319G>A |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:[No Data.] |
| ToMMo:0.360 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:[No Data.] |
Prediction
ClinVar
| Clinical Significance |
risk factor
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
risk factor
|
2015-02-18 | no assertion criteria provided | age related macular degeneration 7 |
germline
|
Detail |
|
risk factor
|
2015-02-18 | no assertion criteria provided | Susceptibility to neovascular type of age-related macular degeneration |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.319 | age related macular degeneration | Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated ge... | BeFree | 23582991 | Detail |
| 0.480 | age related macular degeneration | Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated ge... | BeFree | 23582991 | Detail |
| 0.021 | age related macular degeneration | Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated ge... | BeFree | 23582991 | Detail |
| 0.005 | age related macular degeneration | Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated ge... | BeFree | 23582991 | Detail |
| 0.480 | age related macular degeneration | Highly myopic elderly Japanese patients with and without CNV were genotyped for ... | BeFree | 19680273 | Detail |
| 0.007 | macular degeneration | After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associat... | BeFree | 22491416 | Detail |
| 0.404 | age related macular degeneration | Many single-nucleotide polymorphisms (SNPs), including the previously reported v... | BeFree | 18164066 | Detail |
| 0.267 | age related macular degeneration | SNP rs10490924 on chromosome 10 in exon 1 of the ARMS2 gene showed a highly sign... | BeFree | 19259132 | Detail |
| 0.005 | macular degeneration | The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containin... | BeFree | 18164066 | Detail |
| 0.128 | Exudative age-related macular degeneration | After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associat... | BeFree | 23326481 | Detail |
| 0.185 | age related macular degeneration | In this Korean neovascular AMD cohort, treatment outcome after anti-VEGF was fou... | BeFree | 25558172 | Detail |
| 0.404 | age related macular degeneration | SNP rs10490924 on chromosome 10 in exon 1 of the ARMS2 gene showed a highly sign... | BeFree | 19259132 | Detail |
| 0.007 | macular degeneration | Many single-nucleotide polymorphisms (SNPs), including the previously reported v... | BeFree | 18164066 | Detail |
| 0.404 | age related macular degeneration | The HTRA1 promoter SNP (rs11200638) and A69S at LOC387715/ARMS2 were associated ... | BeFree | 23582991 | Detail |
| 0.267 | age related macular degeneration | The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containin... | BeFree | 18164066 | Detail |
| 0.404 | age related macular degeneration | Highly myopic elderly Japanese patients with and without CNV were genotyped for ... | BeFree | 19680273 | Detail |
| 0.012 | Geographic Atrophy | Comparing combined CNV-GA to GA and CNV only, patients with both had a higher fr... | BeFree | 22699975 | Detail |
| 0.003 | diabetic retinopathy | In HTRA1, rs11200638 (G>A), showed marginal significance with DR (P = 0.055) ... | BeFree | 21067572 | Detail |
| 0.267 | age related macular degeneration | Highly myopic elderly Japanese patients with and without CNV were genotyped for ... | BeFree | 19680273 | Detail |
| 0.404 | age related macular degeneration | After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associat... | BeFree | 22491416 | Detail |
| 0.267 | age related macular degeneration | We genotyped three SNPs, rs1061170 (exon 9, CFH), rs11200638 (HTRA1 promoter, -5... | BeFree | 18682806 | Detail |
| 0.267 | age related macular degeneration | The ARMS2/HTRA1 genes at the 10q26 locus have been associated with risk of age-r... | BeFree | 23592919 | Detail |
| 0.267 | age related macular degeneration | The HTRA1 promoter SNP (rs11200638) and A69S at LOC387715/ARMS2 were associated ... | BeFree | 23582991 | Detail |
| 0.195 | age related macular degeneration | We investigated the frequency of Tyr402His polymorphism of the complement factor... | BeFree | 19845562 | Detail |
| 0.005 | macular degeneration | Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in comp... | BeFree | 24080590 | Detail |
| 0.185 | age related macular degeneration | Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in comp... | BeFree | 24080590 | Detail |
| 0.011 | macular degeneration | Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in comp... | BeFree | 24080590 | Detail |
| 0.480 | age related macular degeneration | Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in comp... | BeFree | 24080590 | Detail |
| 0.480 | age related macular degeneration | Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism ... | BeFree | 24393350 | Detail |
| 0.267 | age related macular degeneration | Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was ... | BeFree | 25277308 | Detail |
| 0.005 | macular degeneration | Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism ... | BeFree | 24393350 | Detail |
| 0.480 | age related macular degeneration | Subject I:2 with AMD carried both at-risk genotypes at HTRA1 rs11200638 and CFH ... | BeFree | 19933189 | Detail |
| 0.034 | Choroidal Neovascularization | [A common genetic background may exist between typical exudative AMD and PCV pat... | GAD | 18939352 | Detail |
| 0.007 | Exudative age-related macular degeneration | Correlation between CFH Y402H and HTRA1 rs11200638 genotype to typical exudative... | BeFree | 18939352 | Detail |
| 0.267 | age related macular degeneration | [Genotype at polymorphism rs11200638 and HTRA1 expression level.] | GAD | 21060055 | Detail |
| 0.267 | age related macular degeneration | An intergenic region between the tagSNP rs3793917 and rs11200638 in the HTRA1 ge... | BeFree | 20445115 | Detail |
| 0.005 | macular degeneration | Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was ... | BeFree | 25277308 | Detail |
| <0.001 | Confluent drusen | In addition, rs11200638 was significantly associated with soft confluent drusen,... | BeFree | 17426452 | Detail |
| 0.240 | Macular Degeneration, Age-Related, 7 | NA | CLINVAR | Detail | |
| 0.267 | age related macular degeneration | HTRA1 promoter polymorphism in wet age-related macular degeneration. | GWASCAT | 17053108 | Detail |
| 0.267 | age related macular degeneration | The association of SKIV2L rs429608 with neovascular AMD remained significant aft... | BeFree | 23260260 | Detail |
| 0.120 | MACULAR DEGENERATION, AGE-RELATED, NEOVASCULAR TYPE, SUSCEPTIBILITY TO | NA | CLINVAR | Detail | |
| 0.267 | age related macular degeneration | Moreover, recent reports have shown that the rs11200638, a single nucleotide pol... | BeFree | 19798546 | Detail |
| 0.480 | age related macular degeneration | The association of SKIV2L rs429608 with neovascular AMD remained significant aft... | BeFree | 23260260 | Detail |
| 0.011 | macular degeneration | Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism ... | BeFree | 24393350 | Detail |
| 0.267 | age related macular degeneration | Subject I:2 with AMD carried both at-risk genotypes at HTRA1 rs11200638 and CFH ... | BeFree | 19933189 | Detail |
| 0.005 | macular degeneration | The association of SKIV2L rs429608 with neovascular AMD remained significant aft... | BeFree | 23260260 | Detail |
| 0.011 | macular degeneration | The association of SKIV2L rs429608 with neovascular AMD remained significant aft... | BeFree | 23260260 | Detail |
| 0.267 | age related macular degeneration | Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism ... | BeFree | 24393350 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_002775.4(HTRA1):c.-625G>A AND Age related macular degeneration 7 | ClinVar | Detail |
| NM_002775.4(HTRA1):c.-625G>A AND Susceptibility to neovascular type of age-related macular degenerat... | ClinVar | Detail |
| Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated genes including CFH (r... | DisGeNET | Detail |
| Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated genes including CFH (r... | DisGeNET | Detail |
| Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated genes including CFH (r... | DisGeNET | Detail |
| Seventeen single nucleotide polymorphisms (SNPs) in known AMD risk-associated genes including CFH (r... | DisGeNET | Detail |
| Highly myopic elderly Japanese patients with and without CNV were genotyped for three AMD-associated... | DisGeNET | Detail |
| After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associated with exudative AM... | DisGeNET | Detail |
| Many single-nucleotide polymorphisms (SNPs), including the previously reported variants rs10490924 (... | DisGeNET | Detail |
| SNP rs10490924 on chromosome 10 in exon 1 of the ARMS2 gene showed a highly significant association ... | DisGeNET | Detail |
| The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containing rs10490924 and rs1... | DisGeNET | Detail |
| After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associated with nAMD and PCV... | DisGeNET | Detail |
| In this Korean neovascular AMD cohort, treatment outcome after anti-VEGF was found to differ by the ... | DisGeNET | Detail |
| SNP rs10490924 on chromosome 10 in exon 1 of the ARMS2 gene showed a highly significant association ... | DisGeNET | Detail |
| Many single-nucleotide polymorphisms (SNPs), including the previously reported variants rs10490924 (... | DisGeNET | Detail |
| The HTRA1 promoter SNP (rs11200638) and A69S at LOC387715/ARMS2 were associated with a poorer visual... | DisGeNET | Detail |
| The coding HTRA1 SNP rs2293870, not part of the significant haplotypes containing rs10490924 and rs1... | DisGeNET | Detail |
| Highly myopic elderly Japanese patients with and without CNV were genotyped for three AMD-associated... | DisGeNET | Detail |
| Comparing combined CNV-GA to GA and CNV only, patients with both had a higher frequency of at-risk a... | DisGeNET | Detail |
| In HTRA1, rs11200638 (G>A), showed marginal significance with DR (P = 0.055) while rs10490924 in ... | DisGeNET | Detail |
| Highly myopic elderly Japanese patients with and without CNV were genotyped for three AMD-associated... | DisGeNET | Detail |
| After adjusting for rs11200638, ARMS2 rs10490924 remained significantly associated with exudative AM... | DisGeNET | Detail |
| We genotyped three SNPs, rs1061170 (exon 9, CFH), rs11200638 (HTRA1 promoter, -512 bp), and rs104909... | DisGeNET | Detail |
| The ARMS2/HTRA1 genes at the 10q26 locus have been associated with risk of age-related macular degen... | DisGeNET | Detail |
| The HTRA1 promoter SNP (rs11200638) and A69S at LOC387715/ARMS2 were associated with a poorer visual... | DisGeNET | Detail |
| We investigated the frequency of Tyr402His polymorphism of the complement factor H (CFH) gene, Ser69... | DisGeNET | Detail |
| Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in complement factor H (CFH... | DisGeNET | Detail |
| Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in complement factor H (CFH... | DisGeNET | Detail |
| Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in complement factor H (CFH... | DisGeNET | Detail |
| Genotypes of 3 polymorphisms in known AMD susceptibility loci (rs1061170 in complement factor H (CFH... | DisGeNET | Detail |
| Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism pathway and 2 known ... | DisGeNET | Detail |
| Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was also predisposed ris... | DisGeNET | Detail |
| Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism pathway and 2 known ... | DisGeNET | Detail |
| Subject I:2 with AMD carried both at-risk genotypes at HTRA1 rs11200638 and CFH rs800292. | DisGeNET | Detail |
| [A common genetic background may exist between typical exudative AMD and PCV patients.] | DisGeNET | Detail |
| Correlation between CFH Y402H and HTRA1 rs11200638 genotype to typical exudative age-related macular... | DisGeNET | Detail |
| [Genotype at polymorphism rs11200638 and HTRA1 expression level.] | DisGeNET | Detail |
| An intergenic region between the tagSNP rs3793917 and rs11200638 in the HTRA1 gene indicates associa... | DisGeNET | Detail |
| Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was also predisposed ris... | DisGeNET | Detail |
| In addition, rs11200638 was significantly associated with soft confluent drusen, which are strongly ... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| HTRA1 promoter polymorphism in wet age-related macular degeneration. | DisGeNET | Detail |
| The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| Moreover, recent reports have shown that the rs11200638, a single nucleotide polymorphism (SNP) in t... | DisGeNET | Detail |
| The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... | DisGeNET | Detail |
| Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism pathway and 2 known ... | DisGeNET | Detail |
| Subject I:2 with AMD carried both at-risk genotypes at HTRA1 rs11200638 and CFH rs800292. | DisGeNET | Detail |
| The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... | DisGeNET | Detail |
| The association of SKIV2L rs429608 with neovascular AMD remained significant after adjusting for CFH... | DisGeNET | Detail |
| Eight single nucleotide polymorphisms (SNPs) from 6 genes of the HDL metabolism pathway and 2 known ... | DisGeNET | Detail |
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs11200638 dbSNP
- Genome
- hg38
- Position
- chr10:122,461,028-122,461,028
- 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))
- rs11200638
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.36
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6032
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16756
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