@SunilDe just in case this helps, wanted to share this post about 4 places timeouts may be set http://community.retool.com/t/query-timeout-where-to-look/16604 (note numbers 2 and 3 are specific to self-hosted instances of Retool. Could it be possible that there's a timeout setting on your database level, outside of Retool? 
What kind of resource are you querying?