Found this article/research. Just cant find the gene or SNP they are refering to in 23andME. Anyone else after readin this have an idea which gene SNP (s) they are refering to, I would like to look up in raw data. I have has neurotransmitter issues for years so I am curious how my genes line up with this research.
http://www.cfids-cab.org/cfs-inform/Genes/narita.etal03.pdf
For a lot of SNPs there aren't RS numbers (or weren't when this study was run), so things are described based on their location. In this case the gene is using an old name, which makes things harder. If you go to
www.ncbi.nlm.nih.gov/gene/ and search for "5-HTTLPR", the first result (SLC6A4) has that listed as an alternative name.
Then it says this abnormality is in the "5' upstream region", which means it's at one end of the gene. If you're on the gene page, you can go to the "map" and scroll til the left end of the gene is in the center of the screen, then zoom in a bit. If you click on the rsIDs which appear, you can see (right above their map on the new page) that their "Function" is given as "UTR-5". So you're in the right neighborhood, and the results they're talking about are somewhere in that part of the gene where it's showing the thicker band.
Unfortunately, it's hard to make a direct comparison between that study and your 23andMe results. That study is looking at an entire "sentence", whereas 23andMe is just sampling a few letters from that sentence. But they're looking at length of sequences, which might suggest an insertion or deletion SNP. So it might be possible to check all of the UTR-5 SNPs to see if any are deletion or insertion SNPs, or check your results from that gene in your 23andMe results to see if there's any DD, II, DI, or maybe even -- results.
The only 23andMe SNPs in the UTR-5 are rs28914824 and rs25533. Though a few more are shortly after it and listed as being associated with the gene when viewing them: rs28914823, rs2321495, rs25532, rs25531, rs28914822. You can also search for the priming sequences using the gene view to get the actual location on the chromosome.
The first flanking sequence ends at 28,564,494 and the 2nd flanking sequence starts at 28,564,007. If you zoom out until you can see that entire range, there's a bunch of SNPs in there with data about them. You can also look for those ranges (on chromosome 17) on your 23andMe results to see which SNPs are reported that are in that range: rs25532 and rs25531.
For rs25532 I have the normal "GG" and for rs25531 I have "--". Does the "--" mean I have something other than an expected result, possibly as the result of an earlier insertion or deletion? No idea!
The study doesn't give the alternative allele sequence, only stating that it's longer. And even if it did give the alternative, I still have the "--" which isn't going to help me anyhow.