I work with similar type of data (I work for Genus Plc.) So we have SNP and phenotype data to store also.
Our needs are very similar, but we have a local cluster we use for our genetic discovery research.
I'm looking into a NoSQL alternative to house genotype data and hopefully, add phenotype and mine the data for all sorts of things.
Our datasets are pretty large too. I've been looking at a few DBs: MongoDB, HadoopDB and Cassandra. So far I like cassandra the most, but still testing it.
Sorry I'm not really answering your question other than to say: we're also looking at this. :)
I'd like to stay in touch, perhaps even work together on developing a solution.
-Fernie