There is pretty much a 100% probability that I carry Neandertal origin genes, since I’m Eurasian. That being said, I hadn’t looked too closely into the matter in regards to my own genome, because the whole “which SNPs are Neandertal” issue has been pretty dicey. But after the “Neandertal dystrophin” paper sniffing for whether you carry a specific Neandertal haplotype got a whole lot easier. The authors provided the markers and their associated haplotypes within the paper. So if the B006 haplotye is Neandertal, by looking at your markers in 23andMe through the browse raw data feature you can figure out what your lineage is, and see if you are indeed “Neandertal” on that locus. Since it’s on the X chromosome, males will carry only one copy of the gene. On the other hand, if you’re a woman you’ll have two copies, so ascertaining what specific combination of markers you have spanning a particular genomic segment can be more difficult (the results are not “phased,” so you don’t know if the allele is from the mother or father on any given genotype). But inferring the sequence of markers on a strand of DNA is much easier if you have relatives to compare with.
As you know the results for my first sibling came back earlier this week. I decided to look at which haplotypes we carried. Below the fold are the SNPs (the links will take you to 23andMe, so if you are logged into your account it will take you to where you need to go):