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JR Hokkaido

JR East
JR Central
JR West
JR Shikoku
JR Kyushu

Tokyu railway
southwest Tokyo urban   
connection : Yokohama, Daikanyama, Jiyugaoka, Shibuya
 
Odakyu railway
southwest Tokyo urban   
connection : Hakone, Izu, Enoshima, Shinjuku
Keio railway
west Tokyo urban
connection : Mt. Takao, Sanrio Puroland, Ajinomoto Stadium, Shinjuku
Keikyu railway
south Tokyo urban 
connection : Haneda airport, Asakusa and Ginza ( through metro ) , Shinagawa
Keisei railway
northeast Tokyo urban and Chiba
connection : Narita airport, Ueno, Nakayama Racecource
Seibu railway
northwest Tokyo urban and Saitama  
connection : Kawagoe, Chichibu, Toshimaen, Seibu Dome, Ikebukuro
Tobu railway
north Tokyo urban and Saitama, Tochigi, Gunma 
connection : Nikko, Kinugawa-Onsen, Tokyo Sky Tree
Tokyo Monorail
Hamamatsucho - Haneda airport  
connection : Haneda airport, Tennozu
Rinkai Line   ( Tokyo Waterfront area Rapid transit )
Osaki - Shinkiba  
connection : Odaiba, Tokyo Big Sight
Yurikamome
Shinbashi - Toyosu 
connection : Odaiba, Tokyo Big Sight, Oedo-Onsen-Monogatari
Tsukuba express
Akihabara - Tsukuba  
connection : Tsukuba university

Hankyu railway
Kobe - Osaka - Kyoto   
connection : MIno, Takarazuka, Rokko, Oji zoo, Arashiyama, Nagaoka-Tenjin
Hanshin railway
Kobe - Osaka - Nara  
connection : Koshien stadium, Osaka Dome, Amagasaki
Keihan railway
Osaka - Kyoto  
connection : Kyoto, Fushimi, Kyobashi
Nankai railway
south Osaka  
connection : Kansai airport, Koyasan, Wakayama, Namba
Kintetsu railway
east and southeast Osaka and Nara, Osaka - Nagoya  
connection : Nara, Iseshima, Nagoya, Kyoto, Osaka

Meitetsu railway
Nagoya urban   
connection : Chubu airport, Inuyama, Nagoya