Why Can'T I Find Certain Snp Names In Dbsnp?

Question

[bdeonovic]

We did some DNA sequencing and then did some GWAS analysis (using PLINK). Some of the SNPs in the MAP file look like:

exm1166050
exm984699
kgp6761044

But when I search for these in dbSNP I find nothing. There are also SNPs that have the more familiar rs#'s (e.g. rs4756277) I believe we used Illumina's HumanOmniExpress BeadChip Kit for the DNA sequencing.

What are these SNPs? Is there some different naming to them?

Also look at this:

https://stat.ethz.ch/pipermail/bioconductor/2012-October/048480.html

this is how to find RS# if you have chr and bp-position: http://www.ncbi.nlm.nih.gov/books/NBK44454/#Search.how_do_i_search_dbsnp_for_the_tot

Answer 1

[Tky]

Apparently they are not dbSNP identifiers.

I think there is difference in the definition of SNP and mutations ( Please correct me if I am wrong) SNP, single-nucleotide polymorphism is defined the variant has certain frequency in general population, generally with minor allele frequency >1%. On the other hand, the rare variant identified in whole exome sequencing or whole genome sequencing might be seen in one or several individuals, and may not be counted as SNP.

So back to your question, variants you listed like exm1166050 might from some in-house exome database and is not registered in dbSNP.