[Genome] Finding gene information from command line

[Cory Y. McLean]

Hi,


I’ve been trying to determine the locations of SNPs such as whether or not
they are intergenic or coding(synonymous and non-synonymous). So let’s take
the following example:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=87429801&hgt.in1=1.5x&position=chr1%3A19811681-19811691

Say I am looking at a SNP at location chr1:19,811,685. I can see that the
normal base at this position is A, and that the amino acid for the gene
that is at this position is a C. I was wondering if there is any way to get
these two pieces of information in a text format, ie I can make a query for
chr1:19,811,685 and get base:A, the associated codon, and the resulting
amino acid as well as the direction of transcription.

I looked in the knownGene table for hg17 and see that I can find the genes
that have exons that overlap this position, and that include strand
information, but am wondering if there is a table that holds amino acid
information as well.

thanks!

-Cory