Tokyo's main commuting lines, JR Yamanote  line and Keihin Tohoku line (connecting from Kanagawa) are suspended on the morning of January 16. 
They are slowly recovering and Yamanote is due to recover in the afternoon, but there are entry restricrions at some stations and delays on trains.

There are metros and buses available otherwise.

For travelers: Watch for more information on JR website.

Train Status Information | JR-EAST

関東エリアの運行情報・運休情報：JR東日本