Find genes which are related to SNPs

Question

[hosin]

Hi

Is there any chance to get SNPEff or some files which work like that in NCBI or other dataset? Actually I just want to find genes related to SNPs which are in a map file based on Oar_v4.0 or Oar_v3.1 reference genomes. I need some files like that.

My file is:

Chr Snp     Cm  Pos
1   rs400427694 0   20509
1   rs415239111 0   21717
2   rs408999184 0   206544601
2   rs417013160 0   206552175
3   rs418489595 0   141890679
4   rs430807116 0   102637344
4   rs429176809 0   102641170

[GenoMax]

What organism are these rsID's from? They no longer appear to be in NCBI. What is Oar_v4.0?

[Nicolas Rosewick]

OAR = ovis aries = sheep

Answer 1

[GenoMax]

Your best bet is to use variation resources from Ensembl: http://www.ensembl.org/Ovis_aries_rambouillet/Info/Index