Question: Clinically Relevant Snps In The Neighborhood Of Gwas Signal
gravatar for jeffrey.mitchel
6.0 years ago by
jeffrey.mitchel0 wrote:

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 • 1.9k views
ADD COMMENTlink modified 6.0 years ago by Michael Dondrup47k • written 6.0 years ago by jeffrey.mitchel0

Try HaploReg.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by zx87549.0k
gravatar for Pierre Lindenbaum
6.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

Using the ucsc mysql server:

$ mysql --user=genome -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               |
ADD COMMENTlink written 6.0 years ago by Pierre Lindenbaum126k
gravatar for Michael Dondrup
6.0 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

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.

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Michael Dondrup47k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1467 users visited in the last hour