Make sure that all the GST Returns are filed up to date and no liability is pending with the Department before you proceed to cancel your GST Registration.
After you file all your GST Returns ( with the applicable late fees, if any ) , then you will find the option of cancellation of GST Registration in the portal.
You have to file FORM GST REG-16 ( Application for Cancellation of GST Registration ).
I opted for Quarterly GST Return and 6 month nil return completed in July month. GSTR 3B is filed but can not file GSTR 1 as due in Oct month. Also there is late fees of June GSTR 1 Which will be paid in subsequent GSTR 1.