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Old 11-23-2015, 02:09 AM   #1
esuarp
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Location: Switzerland

Join Date: Nov 2015
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Default 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:

position
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


Lukas
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Old 11-23-2015, 03:39 AM   #2
mastal
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Have you tried the UCSC genome browser?

https://genome.ucsc.edu/index.html

You have to check that you use the same version of the human genome assembly that your data is from.
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Old 11-23-2015, 03:47 AM   #3
GenoMax
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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?
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Old 11-23-2015, 04:46 AM   #4
esuarp
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@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?
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Old 11-23-2015, 04:51 AM   #5
mastal
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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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