I thought the timeout was 30 seconds - if you look in your Chrome Dev Tools console, do you get a more detailed error there? (Or in the grafana server logs).
Long queries is very much an edge case for Grafana. Most timeseries queries should complete within in a second or two.
There is a feature request for adding a configuration option for query timeouts but it is not implemented: https://github.com/grafana/grafana/issues/3168