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From SNPedia

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
ReferenceGRCh38 38.1/141
GeneLOC105375015, LOC107984144, LOC107984145, LOC107984146
is asnp
is mentioned by
dbSNP (classic)rs9264942
1000 genomesrs9264942
23andMe allrs9264942
GWAS Ctlgrs9264942
Max Magnitude2.2
? (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 17641165OA-icon.png] 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 20041166OA-icon.png]
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 21051598OA-icon.png]
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 18256235OA-icon.png] WGAViewer: software for genomic annotation of whole genome association studies.

[PMID 18982067OA-icon.png] 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 19107206OA-icon.png] Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study.

[PMID 19276793OA-icon.png] Host genetics and HIV-1 viral load set-point in African-Americans.

[PMID 20552027OA-icon.png] Host and viral genetic correlates of clinical definitions of HIV-1 disease progression.

[PMID 21221856OA-icon.png] The search for host genetic factors of HIV/AIDS pathogenesis in the post-genome era: progress to date and new avenues for discovery.

[PMID 21499264OA-icon.png] 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 22474614OA-icon.png] Host Genes Important to HIV Replication and Evolution.

GWAS snp
PMID [PMID 23128233OA-icon.png]
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 23543094OA-icon.png] Testing for associations between loci and environmental gradients using latent factor mixed models.

[PMID 24842830OA-icon.png] Regulatory variation in HIV-1 dependency factor ZNRD1 associates with host resistance to HIV-1 acquisition

[PMID 25083782OA-icon.png] HLA-C -35kb Expression SNP Is Associated with Differential Control of β-HPV Infection in Squamous Cell Carcinoma Cases and Controls

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 32709981OA-icon.png] Polymorphism at rs9264942 is associated with HLA-C expression and inflammatory bowel disease in the Japanese.