rs9264942
How much HLA-C you display, and HIV control
What this position does
HLA molecules hold up fragments of what is inside your cells for immune inspection. This position controls how much HLA-C is displayed, and people who display more of it control HIV infection considerably better without treatment. It is one of the clearest single-variant effects on any infectious disease.
Immune system. Shaped by viral infection. This is one of the variants that differs sharply between human populations, because something in the environment made one version worth having.
Infection, and the cost of fighting it
For most of human history the commonest way to die young was infection. An immune system tuned to win those fights is tuned for a world that, in rich countries, no longer exists.
What changed: Industry, roughly the last two centuries. Indoor work, heated buildings, refined food, cheap salt and sugar, tobacco at scale, and a collapse in infectious disease. This is where most of the deals in your genome came undone.
Why it spread: a strong case, not settled. There is a clear signal of recent selection and a widely favoured explanation for it, which is not the same as a proven one.
Spiral Staircase, chapter 20: The Fever and the Old Enemies Spiral Staircase is written by the same author as this site.
What each result means
| If you carry | What it means |
|---|---|
| No copies of the effect version TT | You display less HLA-C The lower-expression version on both copies. |
| One copy CT | You carry one higher-expression copy Intermediate expression. |
| Two copies CC | You display more HLA-C The higher-expression version, associated with better spontaneous control of HIV and, separately, with a somewhat higher risk of Crohn's disease. Displaying more of yourself to your immune system cuts both ways. |
How common each version is
| Ancestry group | C (the effect version) | |
|---|---|---|
| African | 27.0% | |
| American | 30.4% | |
| East Asian | 39.3% | |
| European | 36.2% | |
| South Asian | 52.5% |
1000 Genomes Project phase 3, via Ensembl, retrieved 2026-09-23. These groupings are coarse and flatten a great deal of internal diversity, particularly within Africa. A variant being common somewhere tells you where a piece of your ancestry probably comes from, and nothing else.
How many people carry each result
| Ancestry group | TT | CT | CC |
|---|---|---|---|
| African | 351 / 661 | 263 / 661 | 47 / 661 |
| European | 200 / 503 | 242 / 503 | 61 / 503 |
| East Asian | 185 / 504 | 242 / 504 | 77 / 504 |
| South Asian | 114 / 489 | 237 / 489 | 138 / 489 |
| American | 170 / 347 | 143 / 347 | 34 / 347 |
Counts of people, not modelled frequencies: every one of the 2,504 individuals sequenced by the 1000 Genomes Project phase 3, tallied by the genotype they carry. Deriving these from allele frequencies instead would assume random mating inside each group and undercount the homozygotes.
How to find out which you have
If you have taken a test with 23andMe, AncestryDNA, MyHeritage, Family Tree DNA, TellMeGen or Living DNA, this position is very likely already in the raw data file they gave you. You do not need another test.
One thing to watch if you look it up by hand: testing companies report some positions from one DNA strand and some from the other, and the file does not say which. Read the letters as they appear and you will get the opposite of the truth for some positions. Sequencings resolves that automatically.
Source
Coordinates and allele pair verified against Ensembl GRCh37. Direction of effect verified against VEP protein consequences or 1000 Genomes population frequency. Category: Population adaptation.
Common questions
What is rs9264942?
rs9264942 is a position in the near HLA-C gene on chromosome 6. HLA molecules hold up fragments of what is inside your cells for immune inspection. This position controls how much HLA-C is displayed, and people who display more of it control HIV infection considerably better without treatment. It is one of the clearest single-variant effects on any infectious disease.
What does it mean if I have CC at rs9264942?
You display more HLA-C. The higher-expression version, associated with better spontaneous control of HIV and, separately, with a somewhat higher risk of Crohn's disease. Displaying more of yourself to your immune system cuts both ways.
What does it mean if I have TT at rs9264942?
You display less HLA-C. The lower-expression version on both copies.
How do I find out my rs9264942 genotype?
If you have taken a home DNA test, this position is very likely in the raw data file you were given. Sequencings reads that file in your browser without uploading it, and resolves which DNA strand each position was reported from, which is the step most manual lookups get wrong.
This is reference information, not medical advice, and not a diagnosis. See the medical disclaimer. Category: Population adaptation.