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Clinically Relevant Snps In The Neighborhood Of Gwas Signal

I'm a grad student wrapping up a GWAS study (first one I've ever been involved in) and I have a handful of interesting signals. However, the SNPs at the top of those signals don't really turn up anything in Google. Are there any databases I can look at or tools I could use to help me find clinically relevant SNPs that might be in the neighborhood of the significant SNPs found in my study?

I have Googled the genes my SNPs are in, and of course I am able to find information on those, but I was wondering it there is a popular tool to input my rs##### for some SNPs, and it returns well-documented, clinically relevant SNPs that are near it.

I imagine this is a very rudimentary question, but I'm pretty new to GWAS and am getting used to the workflow. I have all these significant SNPs, but at this moment, I'm kind of at the "who cares?" stage where I need to talk about why my findings are important (because they are, dang it!)

gwas snp
• 3,052 views • link
updated by Michael Dondrup Michael Dondrup • written by jeffrey.mitchel • jeffrey.mitchel

2 answers

Using the ucsc mysql server:

$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select chrom,chromStart,chromEnd,name,bitfields from snp138 where chrom="chr1" and chromStart>=985950 and chromEnd< 1635350 and FIND_IN_SET("clinically-assoc",bitfields ) >0'
+-------+------------+----------+-------------+--------------------------------------------------+
| chrom | chromStart | chromEnd | name        | bitfields                                        |
+-------+------------+----------+-------------+--------------------------------------------------+
| chr1  |     985954 |   985955 | rs199476396 | clinically-assoc,has-omim-omia,submitted-by-lsdb |
| chr1  |    1199488 |  1199489 | rs207460006 | clinically-assoc,has-omim-omia,submitted-by-lsdb |
| chr1  |    1245103 |  1245104 | rs144003672 | clinically-assoc,submitted-by-lsdb               |
| chr1  |    1265153 |  1265154 | rs307355    | clinically-assoc,has-omim-omia                   |
| chr1  |    1265459 |  1265460 | rs35744813  | clinically-assoc,has-omim-omia                   |
| chr1  |    1469330 |  1469331 | rs145324009 | clinically-assoc,submitted-by-lsdb               |
| chr1  |    1635334 |  1635335 | rs201004006 | clinically-assoc,submitted-by-lsdb               |
+-------+------------+----------+-------------+--------------------------------------------------+
• 133 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

SNPedia is a good starting point. In its link-out it lists a lot of other resources as well. Also, I would use LD as a measure of distance instead of physical distance.

• 269 views • link
written by Michael Dondrup Michael Dondrup

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