I hope I understand your question: The UCSC genome database contains the position in both base index and cM for the STS. e.g.:

~> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg18 -e 'select name,chrom,chromStart,chromEnd,genethonPos from stsMap where genethonPos!=0 limit 2\G'
*************************** 1. row ***************************
       name: AFM280WE5
      chrom: chr1
 chromStart: 3574721
   chromEnd: 3575045
genethonPos: 6.2
*************************** 2. row ***************************
       name: AFM344WE9
      chrom: chr1
 chromStart: 4358261
   chromEnd: 4358654
genethonPos: 11.1

So you can use this STS map as a 'reference' to map your collection of SNP from bp to cM.

The Rutgers Map has an interpolate feature that can be used for any SNP not too near the telomeres or centromere. http://compgen.rutgers.edu/RutgersMap/InterpolateMap.aspx

Hey Pierre,

Thanks for your answer! I already got the genetic map provided by USCS database with STS markers. But my issue remains the same: the density of markers of the available genetic maps (the USCS one or HapMap II one) is much lower than the density of my SNP set. For example I have 4054 SNPs between the 2 STS markers above (in your comment).

Therefore I don't know how to attribute to each SNPs of my set a position in cM without doing a very important approximation.

Anyway, what do you suggest? To use a rule of three approach to attribute a cM position to my collection's SNPs?

Thanks for your advice!

Pierre