Hi! We are now trying to understand, what Illumina chip is better for medical condition testing. So I used this MySQL query to get list of clinically-associated SNP':
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e ' SELECT * FROM snp132 s WHERE s.bitfields LIKE 'clin%' '
So now I have a list of about 22000 rs and it is interesting what association is meant by the base. There was a question on Biostar (http://biostar.stackexchange.com/questions/1289/disease-associated-snps) that could help me, but since 16 july OMIM table is not more in genome database. And the question is how can I get a list of disases/conditions from this snp list?