When the Neandertal genome was published last year, one of the stories from it was that modern non-Africans have some Neandertal genes. At his blog, John Hawks says that "we don't know whether genetic similarities between Neandertals and present non-Africans are the same in different areas outside Africa" and he sets out to look through the data to determine that. Using HapMap data, he compares Neandertal haplotypes to those of the CEU, YRI, MKK, and LWK samples. "When I find a haplotype shared with the Neandertal in Europe but not in Africa, I'll take that as a candidate haplotype for Neandertal ancestry," he writes. On the X chromosome, Hawks says there are nearly 400 regions in which a Neandertal haplotype is identical to a CEU haplotype and the one with the strongest signature is part of gene associated with Duchenne's muscular dystrophy.
In a second post, Hawks reports that "haplotypes from Neandertals that are common in Europe — say, with more than two or three copies — are mostly rare in China. And vice-versa; haplotypes that are common in CHB are rare in CEU."