rs9264942
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (C;C) | 2.2 | 90% reduction in HIV viral load |
| (C;T) | 2.1 | 60% reduction in HIV viral load |
| (T;T) | 0 | normal |
| Reference | GRCh38 38.1/141 |
| Chromosome | 6 |
| Position | 31306603 |
| Gene | LOC105375015, LOC107984144, LOC107984145, LOC107984146 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs9264942 |
| dbSNP (classic) | rs9264942 |
| ClinGen | rs9264942 |
| ebi | rs9264942 |
| HLI | rs9264942 |
| Exac | rs9264942 |
| Gnomad | rs9264942 |
| Varsome | rs9264942 |
| LitVar | rs9264942 |
| Map | rs9264942 |
| PheGenI | rs9264942 |
| Biobank | rs9264942 |
| 1000 genomes | rs9264942 |
| hgdp | rs9264942 |
| ensembl | rs9264942 |
| geneview | rs9264942 |
| scholar | rs9264942 |
| rs9264942 | |
| pharmgkb | rs9264942 |
| gwascentral | rs9264942 |
| openSNP | rs9264942 |
| 23andMe | rs9264942 |
| SNPshot | rs9264942 |
| SNPdbe | rs9264942 |
| MSV3d | rs9264942 |
| GWAS Ctlg | rs9264942 |
| GMAF | 0.3485 |
| Max Magnitude | 2.2 |
| ? | (C;C) (C;T) (T;T) | 28 |
|---|---|---|
|
| ||
This SNP (C/T) is in 5' region of the HLA-C gene, 35 kb away from transcription initiation in or around the HLA-C gene.
"People with this tiny sequence variation, dubbed rs9264942, appear to have up to 90% less virus in their systems than those who carry other polymorphisms. About 10% of Europeans appear to carry two copies of rs9264942, which leads to an average 90% viral load reduction. About 50% of Europeans carry one copy, which gives a 60% reduction. By comparison, less than 40% of people of African descent appear to carry a single copy of the polymorphism." Genetic variation may lower HIV load by 90%
They are referring to the (C;C) genotype giving a 90% reduction and the (C;T) giving a 60% reduction. dbSNP page
This SNP is also reported [PMID 17641165
] to account for 6.5% of the 15% variation in viral load set point in asymptomatic HIV infected individuals. rs2395029 can also be associated with reduced HIV viral load set point.
| GWAS snp | |
|---|---|
| PMID | [PMID 20041166]
|
| Trait | HIV-1 control |
| Title | Common Genetic Variation and the Control of HIV-1 in Human |
| Risk Allele | |
| P-val | 6E-12 |
| Odds Ratio | NR NR |
[PMID 21067287] Multiple sclerosis risk markers in HLA-DRA, HLA-C, and IFNG genes are associated with sex-specific childhood leukemia risk
| GWAS snp | |
|---|---|
| PMID | [PMID 21051598]
|
| Trait | |
| Title | The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation |
| Risk Allele | C |
| P-val | 3E-35 |
| Odds Ratio | 2.9000 [NR] |
[PMID 18256235] WGAViewer: software for genomic annotation of whole genome association studies.
[PMID 18982067] HIV-1 disease-influencing effects associated with ZNRD1, HCP5 and HLA-C alleles are attributable mainly to either HLA-A10 or HLA-B*57 alleles.
[PMID 19050382] Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection.
[PMID 19107206] Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study.
[PMID 19276793] Host genetics and HIV-1 viral load set-point in African-Americans.
[PMID 20552027] Host and viral genetic correlates of clinical definitions of HIV-1 disease progression.
[PMID 21221856] The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery.
[PMID 21499264] Differential microRNA regulation of HLA-C expression and its association with HIV control.
[PMID 21860345] Rising HIV-1 viral load set point at a population level coincides with a fading impact of host genetic factors on HIV-1 control.
[PMID 22474614] Host Genes Important to HIV Replication and Evolution.
| GWAS snp | |
|---|---|
| PMID | [PMID 23128233]
|
| Trait | Crohn's disease |
| Title | Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. |
| Risk Allele | C |
| P-val | 5E-28 |
| Odds Ratio | 1.15 [1.107-1.184] |
[PMID 22772778] Quantity of HLA-C surface expression and licensing of KIR2DL+ natural killer cells.
[PMID 23543094] Testing for associations between loci and environmental gradients using latent factor mixed models.
[PMID 24842830] Regulatory variation in HIV-1 dependency factor ZNRD1 associates with host resistance to HIV-1 acquisition
[PMID 25083782] HLA-C -35kb Expression SNP Is Associated with Differential Control of β-HPV Infection in Squamous Cell Carcinoma Cases and Controls
| ClinVar | |
|---|---|
| Risk | Rs9264942(C;C) |
| Alt | Rs9264942(C;C) |
| Reference | Rs9264942(T;T) |
| Significance | Other |
| Disease | HIV-1 viremia |
| Variation | info |
| Gene | LOC105379660 LOC105379667 LOC105375015 |
| CLNDBN | HIV-1 viremia, susceptibility to |
| Reversed | 0 |
| HGVS | NC_000006.12:g.31306603T>C |
| CLNSRC | OMIM Allelic Variant |
| CLNACC | RCV000016036.2, |
[PMID 30102364] A single nucleotide polymorphism upstream of the HLA-C locus is associated with an anti-HCV seronegative state in a high-risk exposed cohort.
[PMID 32709981] Polymorphism at rs9264942 is associated with HLA-C expression and inflammatory bowel disease in the Japanese.
