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Y chromosome SNP´s names and "rs" code.

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Y chromosome SNP´s names and "rs" code.

Postby mediopeixe » Tue Dec 18, 2007 10:51 pm

Hello, Im new on the forum.

Sorry for my english... :roll:

I have a problem. I´m working with Y chromosome SNP´s, from the NRY region (bynary polymorphisms).
For my actual work, i need to know which is the "rs" number of some mutations. I´ve found some of them at the YCC ISOGG page, index for Y DNA SNP´s

In this page are just the "rs" numbers of a few of them, but i need some more that are not on this page. Been looking for them for a lot of time , and I can´t find an equivalence of names.
For example, got the M173 "rs" number, but the M343 number is not at that page.
I would like to know if there´s a way to get the "rs" numbers from the mutation common names.

Thank u so much!

JUAN
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Re: Y chromosome SNP´s names and "rs" code.

Postby blcr11 » Thu Jan 17, 2008 3:08 pm

I'm curious if anyone found an easy way to do this. I couldn't. I thought it should be easy just to go to the chromosome in question from the ncbi web pages, but I couldn't find anything but the rs codes. Surely, no one remembers SNPs by their rs numbers alone. So how do you link up the "common" name with its rs #--easily?
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Re: Y chromosome SNP´s names and "rs" code.

Postby argiedude » Thu Dec 18, 2008 3:28 pm

mediopeixe wrote:I´ve found some of them at the YCC ISOGG page, index for Y DNA SNP´s

In this page are just the "rs" numbers of a few of them, but i need some more that are not on this page. Been looking for them for a lot of time , and I can´t find an equivalence of names.
For example, got the M173 "rs" number, but the M343 number is not at that page.


http://isogg.org/tree/ISOGG_YDNA_SNP_Index08.html

Actually, M343 is found in the above page. It's rs number is rs9786184. I think every possible y-dna SNP should be listed there.

EDIT: He asked that question on December 18, 2007. I'm answering it on December 18, 2008.
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Re: Y chromosome SNP´s names and "rs" code.

Postby mediopeixe » Thu Dec 18, 2008 6:01 pm

Yes I know. But on that date(a year ago!!) they hadn´t still built up the new 2008 tree, which is the one that is current by now and contains new rs numbers that were not present in the 2007 tree i was refering to on my first post.

The 2008 tree was published about May 2008, and so i could solve a great part of my problem with this new tree.
Despite of this, there are some SNPs i needed which are nowadays lacking an rs #. In the 2008 tree, they give a new way to acceed to the sequence of the SNP, the Y-Position, which is the position, given in bp, of the nucleotide change. I just needed to get the sequences, but to get it from this number was very tired. I finally got all the sequences from this URL using the Y-Position.
http://genome.ucsc.edu/cgi-bin/hgc?o=20 ... 80&db=hg18
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Re: Y chromosome SNP´s names and "rs" code.

Postby isogg » Sat Dec 27, 2008 4:27 pm

This page will give you instructions for matching SNPs to rs numbers:

http://www.isogg.org/rssnp.htm
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