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Newbeee needs help ... from the very beginning



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  • Newbeee needs help ... from the very beginning

    Hello World!

    Im a urologist resident in Switzerland starting a project to link known and probably not yet analyzed SNPs with prostate cancer. Besides my biology-courses in university im new to the whole subject. As you can see there is a huge way to go to even understand what I am doing here ...
    Since my superiors have even less clue about genetics there is no real chance of getting any help from them: thats where this forum comes in ! I hope I can ask a few (at the beginning rather simple) questions.

    Can someone tell me where i can find the SNP numbers (rs....) from these positions:

    2p15 62 814 683
    2p15 63 140 832
    2p15 63 177 560
    3p11 87 223 004
    3q26 171 557 211
    3q26 171 592 128
    11q13 68 736 148
    12q13 51 581 014
    17q12 33 204 443
    19q13 56 052 652

    Thanks for your help


  • #2
    Have you tried the UCSC genome browser?


    You have to check that you use the same version of the human genome assembly that your data is from.


    • #3
      Try the NCBI Variation viewer as well (e.g. http://www.ncbi.nlm.nih.gov/variation/view/?q=2p15). Use this overview to orient yourself: http://www.ncbi.nlm.nih.gov/variation/view/overview/

      BTW: I can see the chromosome arm locations in the first column but what are the other numbers?


      • #4
        @mastai: thank you! my first impression is that the ncbi browser is a bit easier to use but i cant compare pros/cons yet.
        In both browsers i cannot find a SNP-ref.Number for 2p15 Position 62.814.683 (i haven't checked the other yet)
        Any ideas where to look else?


        • #5
          I guess the problem is that if you have a novel SNP, then it won't be in the databases (dbSNP, 1000 genomes).


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