I opened the .bashrc file on a system, which includes

export JAVA_HOME=/usr/lib/jvm/java-1.6.0-sun.x86.64

After typing

whereis java

, the system prints out

java: /usr/bin/java /etc/java /usr/lib/java /usr/share/java /usr/share/man/man1/java.1.gz

It seems to me that none of the above path matches the JAVA_HOME set up in bashrc file. Can you let me know why? I am pretty confusing about how to setting up JAVA_HOME and JAVA_PATH

what OS are you using?
if you're using Windows, look at this for a basic and easy tutorial to set your environment varialbes, otherwise, or if you want another way to set them, take a look at this.