Ok, that’s a really broad title for an important area. And it is a problem that we are starting to see addressed more and more with GWAS (genome wide association studies). If you came here hoping that I had solved this, I’m sorry to disappoint you. We are asked all the time for places to look for this kind of information. The relatively new “Phenotypes and Disease Association Tracks” on the human UCSC Genome Browser have been popular in the training sessions we have given (look at the human browser, and check the second group of tracks controls on the page). You can find OMIM data in Ensembl. You can add Morbid Map to your Map Viewer. Another resource that I just found out about is trying to get at the same types of data–but it is available from their interface and also on the HapMap browser.
MutaGeneSys is a tool with a very simple interface at their web site, but the data is also displayed as a track in the GBrowser at HapMap. The goal was to combine HapMap information + OMIM + whole-genome marker correlation data. The news page at HapMap that describes the addition of this track to HapMap says:
Predicted OMIM associations available in GBrowse
The OMIM associations track presents data from the MutaGeneSys database, which links genotype data from HapMap and whole genome association studies with the known disease variants reported by the OMIM database. Example of a region with multiple OMIM associations: Chr1:194923128..194933127