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Hotair balloons rise because hot air inside the balloon is less dense than the cooler air outside of the balloon. The same thing happens in the atmosphere with thunderstorms. The rising air in the thunderstorm cloud is slightly warmer (and slightly less dense) than the surrounding air outside of the cloud and, once the air begins to rise, the cloud can grow to over 70,000 feet tall.
Learn more about the atmosphere in JetStream - An Online School for Weather.