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From SNPedia

In 2010, a "draft sequence" of a Neanderthal genome was published in SCIENCE ([PMID 20448178]). While the paper should be studied in detail prior to accepting its conclusions, some of those conclusions can be summarized as follows:

  • Neanderthals are on average genetically closer to individuals in Eurasia (Europe + Asia) than to individuals in Africa.
  • Between 1 - 4% of the genomes of modern Eurasians are derived from Neandertals.

The identification of SNPs likely to represent variants that have been introduced into modern human's genomes courtesy of Neanderthal ancestors is possible, based on assumptions discussed in the paper. A quick count based on 42 SNPs present on most 23andMe arrays appears to indicate that most Europeans have on average 5 - 10 (out of 42 possible) such SNPs. These SNPs are listed below; columns as follows: SNP/Rs ; AA = Ancestral Allele – shared with chimpanzee genome ; OOA = “Out of Africa” allele, not shared with Africans and in the Neanderthal candidate regions, therefore possibly a result of Neanderthal admixture


Note: All SNP alleles are listed above in dbSNP strand orientation; those marked with "*" are flipped compared to how they were shown in the original publication.

Update: https://you.23andme.com/reports/neanderthal/

In the post-FDA updated version of 23andMe Neanderthal data, the number of variants (markers (SNPs) with the Neanderthal alle) and the number of homozygous markers is reported rather than the percent Neanderthal. Although 1436 markers are tested and thus 2872 variants are possible, the maximum number of variants observed across all 23andMe profiles is 397. The report concludes with genotypes for five markers associated with traits.

SNP AA VA trait