First start with the NCBI phenome genom e integrator tool, Phegeni. It is free and very user friendly. Allows you to select associated traits using p value, r sq.  cut offs. You can then venture into the eQTL browser for quantitative trait loci analysis.

the old genetic association disease database from NCBI which used to be a great tool is no longer available. The datset till aug 2014 from that database is still available for download. 

Also consider GenABEL, ProbABEL and friends (R packages and freestanding); many other R packages and also  PLINK and PLINK-Seq .as well as SNPTEST (http://www.stats.ox.ac.uk/~marchini/software/gwas/gwas.html)  SNPTEST, PLINK and GenABEL can deal with very large datasets.

very helpful answers Ramaswamy Narayanan  and Gerard Tromp  

thank you very much

Rapidminer?

https://rapidminer.com/