Line station prefixes are used to identify stations in the graph. Therefore, the prefixes must be unique. Lines have their official station prefix in parentheses. If a line does not have an official prefix, one is assigned in square brackets.
- JR East lines passing through Central Tokyo
- Short-distance
- ⭕ [YT] Yamanote
- [KT] Keihin-Tōhoku - Negishi
- [CS] Chūō-Sōbu Local
- Mid-distance
- Utsunomiya (Tohoku Main) & Takasaki
- Tōkaidō
- [UT] Ueno-Tōkyo
- [CR] Chūō Rapid
- [YS] Yokosuka - Sōbu Rapid
- [J] Jōban
- Keiyō
- Kawagoe (Eastern Section) - Saikyō (Akabane) - Rinkai
- Shōnan-Shinjuku
- Short-distance
- Tokyo Metro lines
- (C) Chiyoda
- ⭕ (F) Fukutoshin
- ⭕ (G) Ginza
- ⭕ (H) Hibiya
- (M) Marunouchi
- ⭕ (N) Namboku
- (T) Tōzai
- ⭕ (Y) Yūrakuchō
- ⭕ (Z) Hanzōmon
- Toei subway lines
- (A) Asakusa
- ⭕ (E) Ōedo
- ⭕ (I) Mita
- (S) Shinjuku
- Yokohama Municipal
- (B) Blue
- (G) Green
- JR East lines in satellite cities or suburbs
- Yokohama
- Musashino
- Nambu
- Sagami
- Hachikō - Kawagoe (Western Section)
- Ryōmō
- Tsurumi
- Tohoku Direction
- Karasuyama
- Nikkō
- Chuo Direction
- Chūō Main (mid-distance)
- Itsukaichi
- Ōme
- Sobu Direction
- Sōbu Main
- Sotobō
- Uchibō
- Kururi
- Tōgane
- Joban Direction
- Mito
- Narita
- Tokaido Direction
- Itō
- Gotemba (JR Central)
- Keikyu
- (KK) Keikyū Main
- Airport
- Daishi
- Kurihama
- Zushi
- (KK) Keikyū Main
- Keio
- (KO) Keiō
- Keiō New
- Dōbutsuen
- Keibajō
- Sagamihara
- Takao
- (IN) Inokashira
- (KO) Keiō
- Keisei
- (KS:Blue) Keisei Main
- Chiba
- Chihara
- Higashi-Narita
- Kanamachi
- Oshiage
- (KS:Orange) Narita Sky Access
- (KS:Blue) Keisei Main
- Odakyu
- (OH) Odawara
- (OE) Enoshima
- (OT) Tama
- Seibu
- (SI) Ikebukuro lines
- Ikebukuro
- Sayama
- Seibu Chichibu
- Seibu Yūrakuchō
- Toshima
- (SS) Shinjuku lines
- Shinjuku
- Haijima
- Kokubunji
- Seibu-en
- Tamagawa
- Tamako
- (SI) Ikebukuro lines
- Sotetsu
- (SO) Sotetsu Main
- Izumino
- (SO) Sotetsu Main
- Tobu
- (TS) Skytree
- Kameido
- Daishi
- (TI) Isesaki
- Sano
- Koizumi
- Kiryū
- (TM) Nikkō
- Kinugawa
- Utsunomiya
- (TD) Urban Park
- (TJ) Tōjō
- Ogose
- (TS) Skytree
- Tokyu
- (DT) Den-en-toshi
- (IK) Ikegami
- ⭕ (MG) Meguro
- ⭕ (OM) Oimachi
- (TM) Tamagawa
- ⭕ (TY) Toyoko
- (KD) Kodomonokuni
- Other commuter rail lines
- (HS) Hokusō
- Keisei Kantō
- Jōsō
- Ryūgasaki
- Nagareyama
- Rinkai
- Saitama Rapid
- (SR) Shibayama
- (SL) Shin-Keisei
- (TR) Tōyō Rapid
- (TX) Tsukuba Express
- ⭕ (MM) Minatomirai 21
- Monorails and light transit
- Monorails
- [MC] Chiba Monorail
- [DR] Disney Resort
- [MS] Shōnan Monorail
- [MT] Tama Monorail
- [MK] Tokyo Monorail
- People movers
- [PN] New Shuttle
- [PS] Kanazawa Seaside
- [PT] Nippori-Toneri
- (SY) Seibu Yamaguchi
- [PY] Yūkarigaoka
- (U) Yurikamome
- Trams
- (EN) Enoden Tokyu
- (SG) Setagaya
- Arakawa
- Monorails
- Hinterland
- Chichibu Main Line
- Fujikyuko Line
- Cable cars and aerial tramways
- Ōyama Cable Car
- Hodosan Ropeway
- Keio
- Takao Tozan Railway
- Mitake Tozan Cable Car
- Keisei
- Nokogiriyama Ropeway
- Mount Tsukuba Cable Car
- Mount Tsukuba Ropeway
- Akechidaira Ropeway
- Ikaho Ropeway