Consistent Strand Orientation Across Ncbi, Dbsnp, ...?

Question

[mathias.gorski]

I have genome wide data for 1000 persons with SNPs (rs-numbers as identifiers, including positions and chromosome) on GRCh build 37. I have no information about the SNP's strand orientation. So i want to check their strand orientation. I am familiar with 5' and 3' notation, the meaning of "forward" or "plus" orientation and the illumina format for "top" and bottom".

Where can I download genome wide infos on strands for SNPs containing 1. strand information ("+" or "-") and 2. the corresponding alleles to it from dbSNP or NCBI? Should the orientation of dbSNP and NCBI be consistent? Or would you prefer another institution for this download?

Thanks in advance and all the best :) Mathias.

Answer 1

[Pierre Lindenbaum]

use dbsnp135 from the UCSC: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp135.txt.gz

CREATE TABLE `snp135` (
(...)
  `chrom` varchar(31) NOT NULL,
  `chromStart` int(10) unsigned NOT NULL,
  `chromEnd` int(10) unsigned NOT NULL,
  `name` varchar(15) NOT NULL,
(...)
  `strand` enum('+','-') NOT NULL,
  `refNCBI` blob NOT NULL,
  `refUCSC` blob NOT NULL,
 (...)
)