rs35044562
Neanderthal: the chromosome 3 COVID risk haplotype
What this position does
A 50,000-letter stretch of chromosome 3, inherited whole from Neanderthals, turned out to be the single strongest genetic risk factor for severe COVID-19. It is carried by roughly half of people in South Asia, around one in six Europeans, and almost nobody in East Asia.
What each result means
| If you carry | What it means |
|---|---|
| No copies of the effect version AA | You did not inherit this Neanderthal stretch Neither copy carries it. This is the common result in Europe and near-universal in East Asia. |
| One copy AG | You inherited it from one parent One copy of the Neanderthal haplotype, which was associated with a roughly doubled risk of severe COVID-19 in the 2020 analyses, before vaccination and before treatment improved. |
| Two copies GG | You inherited it from both parents Two copies. The same association applies more strongly. The practical meaning now is small: this was measured in an unvaccinated population early in the pandemic, and vaccination moves outcomes far more than this does. |
Worth knowing. Measured in 2020, in unvaccinated people, against the original variants. It is a fascinating piece of history rather than useful medical guidance today.
How common each version is
| Ancestry group | G (the effect version) | |
|---|---|---|
| African | 0.4% | |
| American | 4.5% | |
| East Asian | 0.5% | |
| European | 8.0% | |
| South Asian | 29.6% |
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 | AA | AG | GG |
|---|---|---|---|
| African | 656 / 661 | 5 / 661 | 0 / 661 |
| European | 423 / 503 | 80 / 503 | 0 / 503 |
| East Asian | 499 / 504 | 5 / 504 | 0 / 504 |
| South Asian | 246 / 489 | 197 / 489 | 46 / 489 |
| American | 317 / 347 | 29 / 347 | 1 / 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: Archaic DNA.
Related
- rs10490770 — Neanderthal: chromosome 3 haplotype, second marker
Where this fits
Common questions
What is rs35044562?
rs35044562 is a position in the LZTFL1 region gene on chromosome 3. A 50,000-letter stretch of chromosome 3, inherited whole from Neanderthals, turned out to be the single strongest genetic risk factor for severe COVID-19. It is carried by roughly half of people in South Asia, around one in six Europeans, and almost nobody in East Asia.
What does it mean if I have GG at rs35044562?
You inherited it from both parents. Two copies. The same association applies more strongly. The practical meaning now is small: this was measured in an unvaccinated population early in the pandemic, and vaccination moves outcomes far more than this does.
What does it mean if I have AA at rs35044562?
You did not inherit this Neanderthal stretch. Neither copy carries it. This is the common result in Europe and near-universal in East Asia.
How do I find out my rs35044562 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: Archaic DNA.