pulling genomic coordinates for snps with rsIDs

[Prithvi Raj]

Hi,

I have a list of SNPs (about 30,000) with rsIDs, i want to pull the hg19 genomic coordinates for them.

I was wondering, how can i do it on UCSC genome browser.

Thanks in advance !

Prithvi

UT Southwestern Med Center

Dallas, Texas

---

UT Southwestern Medical Center
The future of medicine, today.

[Pauline Fujita]

Hello Prithvi,

You can do this using the Table Browser however it might be quite slow
- as the snp tables are very large. If you are comfortable using the
command line that would be the best way to do this - as follows:

1. make a text file with a single rs# ID on each line (call this myRsIDs.txt)

2. download snp137.txt.gz from here:
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/

3. Then run the following:
zcat snp137.txt.gz | grep -Fwf myRsIDs.txt > mySnps.txt


If you're not comfortable using the command line you could do your
query in batches (though they would probably need to be small ~ 1000
rsid's at a time or so. For this approach go to the Table Browser
(genome.ucsc.edu/cgi-bin/hgTables). Once there select:

group: Variation and Repeats
track: Common SNPs 137
table: snp137Common

identifiers: click "paste list" (this is the part that will limit your
input and force you to do batches)

output format: selected fields from primary and related tables

and click "get output".

Then in the next menu you can select which fields you want in your
output - probably at least chrom, chromStart, chromEnd, and name.

Hopefully one of those methods works out for you. If you have further
questions please feel free to contact the mailing list again at
gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

> --
>
>
>