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Rail Transport in Japan
The mainline railway system in Japan is operated by six railway companies of JR Group (Japan Railways Group), provides passenger services separately by region as the map below shows.
To find detailed info, route maps, timetables, fares, etc., visit their official web sites in accordance with the area you are planning to travel. For example, if you plan to travel around Niseko in Hokkaido, visit the website of JR Hokkaido.
JR Japan Railways Group
JR Hokkaido Railway Company
JR East Japan Railway Company
JR Tokai Central Japan Railway Company
JR West Japan Railway Company
JR Shikoku Railway Company
JR Kyushu Railway Comapny
Japan Rail Pass
The Japan Rail Pass allows unlimited travel on Japan Rail trains, buses and ferries.
Other Japanese railway companies
In each local area, private railway companies also provide rail transport services.
Wikipedia | List of Railway comapnies in japan
Train Route Finder by Jorudan Co.,Lrd.