I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association. Moreover, for some species, there are not even any functional descriptions. I need this information for mice, rice, and Arabidopsis Thaliana. Can anyone help me? 
Where can I find a database that has phenotype information together with associated SNPs?
gene;gwas
International Mouse Phenotyping Consortium is building a database of phenotypes and knock-outs of mouse. I believe that this database will be fairly complete (20000 knock-outs), but these are knock-outs, not SNPs... There are several mouse GWAS studies, but I am not aware of a database that would pull all the results together.Arabidopsis big GWAS project is called 1001 genomes project. A lot more information about Arabidopsis from individual experiments is collected and maintained by The Arabidopsis Information Resource, however this resource is subscription based, therefore what you need might not be available for free.As mentioned, SNPs of rice were identified and linked to different rice groups in The 3,000 rice genomes project. There is also GWAS done on 512 individuals, not sure if it is sufficient for reliable conclusions (even they claim that they found supersigificant links).Is this what you were searching for?