[Genome] How to get snps locate between the start and end chromosomal location of each gene with Entrez GeneID

[Gao, Shouguo]

It is really useful to connect to mySQL server. Now I have a large snp list, and I am looking for the snps related to a gene list (Entrez Geneid), which locate between 1000 upstream and 500 downstream of genes. The most important thing is to find the start and end chromosomal location of each gene with Entrez GeneID. I used knowngene and knownToLocusLink tables, but got several locations for one Entrez GeneID (Locuslink). 

 

name    locuslink           chro     strand   start      end

uc001aab.1      375690            chr1     -           4558    14764

uc001aac.1      375690            chr1     -           4558    19346

uc001aad.1      375690            chr1     -           4558    7231

uc001aae.1      375690            chr1     -           4558    9622

uc001aaf.1       375690            chr1     -           4832    19672

uc001aag.1      375690            chr1     -           5658    7231

uc001aah.1      375690            chr1     -           6720    19346

uc001aai.1       375690            chr1     -           6720    9622

 

The reason should be that the same Entrez Gene ID matches multiple UCSC known genes (transcript).

 

In NCBI one Entrez GeneID only has one start and end location. Could you please tell me how to solve this issue? Is there any other table for that?

 

Thanks

 

Shouguo