List Of Dbsnp Rsids And Their Positions
3
5
Entering edit mode
11.2 years ago
pufferfish ▴ 290

Where can I get a list of the RSIDs and chromosome locations for a specific dbSNP build? Build 132 in my case

I've tried:

  1. the ftp download site (doesn't seem to be there)
  2. the Ensembl BioMart server (crashes due to out of memory error)

Thanks in advance!

snp dbsnp • 17k views
ADD COMMENT
9
Entering edit mode
11.2 years ago

From the UCSC download site:

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz" |\
gunzip -c |\
cut -d '       ' -f 2,3,4,5
chr1    10326   10327   rs112750067
chr1    10433   10433   rs56289060
chr1    10439   10440   rs112155239
chr1    10439   10440   rs112766696
chr1    10468   10469   rs117577454
chr1    10491   10492   rs55998931
chr1    10518   10519   rs62636508
chr1    10532   10533   rs114315702
chr1    10582   10583   rs58108140
chr1    10827   10828   rs10218492
ADD COMMENT
0
Entering edit mode

where can I find the description of the columns for snp147.txt.gz in the UCSC website ??

ADD REPLY
0
Entering edit mode

http://genome.ucsc.edu/cgi-bin/hgTables setting the proper parameters and click "describe table schema"

ADD REPLY
0
Entering edit mode

This link is broken- probably outdated. Does anybody have an updated link?

ADD REPLY
8
Entering edit mode
11.2 years ago
brentp 24k

You can get this in simple table format from UCSC. http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz

Or from their mysql:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -NA \
    -e "select chrom, chromStart, chromEnd, name from hg19.snp132" hg19 > snp132.hg19.txt
ADD COMMENT
0
Entering edit mode

This link is also broken. Is there an updated link?

ADD REPLY
1
Entering edit mode
11.2 years ago
Chris ▴ 190

It looks as if the table SNPChrPosOnRef stores that piece of information. The database dumps can be downloaded from the dbSNP ftp server.

ADD COMMENT
0
Entering edit mode

Would this information be the same as in the UCSC table suggested above?

ADD REPLY

Login before adding your answer.

Traffic: 1370 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6