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According to the order issued by the National Human Rights Commission (NHRC), the notices have been sent to the chairman of the Railway Board, chief secretary of the Haryana government, and the Director General of Police of the state.
"The notices were sent a couple of days back," a senior official of the rights panel said, on condition of anonymity.
The NHRC has sought a report from them in four weeks.
His body was dumped close to Asaoti village in Faridabad district.
Junaid's brothers, Hashim and Sakir, were injured by a mob which allegedly also hurled communal slurs against them in Ballabgarh area of Faridabad, while they were travelling on a train from Delhi.
His brothers had claimed the attackers had taunted and repeatedly called them "anti-nationals" and "beef eaters".
A reward of Rs two lakh had also been announced for information on the identities of those involved in the killing.