Finding Synonymous Snp In Ld

Question

[Dpsguy]

Sorry if my question seems naive, but I want to find the synonymous snps that are in high LD (say, r-squared > 0.8), with my snp. Preferably something like MarkerInfo that accepts batch input, but MarkerInfo does not tell me the type of snp (missense, synonymous etc). What tool should I use?

[David Quigley]

Note that if you are working from SNP chip data, many of the loci will not be in protein-coding exons. It's a different case if you're working from data derived from nextgen sequencing.

Answer 1

[Khader Shameer]

Have you tried LocusZoom or SNAP ?

I would recommend to use a standard LD program to find SNPs that are in LD with your SNP of interest. Once you are done with this use UCSC Genome browser (for example see this discussion in biostar)), Ensembl Variation API, BioMart with Ensembl Variation or dbSNP annotations (refer to variation functional class) to filter your SNPs as synonymous or non-synonymous. IMHO, Annotation is one of the most important and the most understated component of GWAS, make sure that you use same version of NCBI for your association, LD calculation and annotation.

[Dpsguy]

Thanks for the suggestions Khader! I am currently tilting towards using MarkerInfo for getting the list of snps in LD and then using this list as input to the UCSC table view to filter for synon snps. Please let me know if you think there is a faster way. Of course what I ideally wanted was something like MarkerInfo with the filtering built in.