Snp Query From Ucsc

Question

[Zhshqzyc]

Hello, I want to a list of snps(HG18). The format likes

rs35568883 38782126 A G

I know UCSC, but how to query?

The condition is chr21:38781803-41824906

Answer 1

[Pierre Lindenbaum]

You can use the UCSC mysql server:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select name,chrom,chromStart,chromEnd,observed from snp130 where name="rs35568883"'
+------------+-------+------------+----------+----------+
| name       | chrom | chromStart | chromEnd | observed |
+------------+-------+------------+----------+----------+
| rs35568883 | chr21 |   38782125 | 38782126 | A/G      |
+------------+-------+------------+----------+----------+

Answer 2

[Hiroyuki Mishima]

FYI, programmatic access to the UCSC database are also discussed in the following threads in BioStar.

• Get rs number based on position
• Is There Such A Thing As A Ucsc Api?

Answer 3

[Docroberson]

Or the UCSC table browser if you don't use mysql. http://genome.ucsc.edu/cgi-bin/hgTables?org=Human&db=hg18 Group -> Variation and repeats Track -> SNPs(130) Output Format -> Selected fields from primary and related tables. Then click 'get output' button. On the next screen check the boxes for name, chrom, chromStart, chromEnd and observed. Then click the 'get output' button on that screen.