[Genome] Mapping SNP positions and IDs

[Kiran Annaiah]

Hello there,

 

 

I am trying to map few of my SNP's and extract 100-200bp upstream and
downstream of it.

I was able to figure out how do those using your browser. I was also
able to map other SNP's in the upstream and downstream regions.

 

I am doing this so I can avoid using those regions when designing my
primer.

 

 

But the one drawback I saw was that (specific to my problem), in the
fasta sequence file is that, it does not tell me what the rsID's of the
mapped SNPs. I would also like to know the alleles (example: [a/t]) at
that particular SNP location.

 

Is there a way I can do this using the browser or atleast submit a batch
query with my rsID's and obtain all the SNPs which fall within the
upstream and downstream region of the sequence I need to use for
designing my primers.

 

The reason I needed the allele info [A/t] at the SNP locations is to
submit it to a specific machine we use here.

 

Any suggestions and ideas would be great. We have hundreds of SNPS to
query and would be a pain to do it manually. I AM trying to see if I
could write a script to automate this process.

 

Thank you

 

Regards

Kiran

 

Dept of Human Genetics

University of Chicago

 

773-391-1208