quick & dirty comparison of MBTA commuter rail fare zones with JR East fares from Shinjukupic.twitter.com/54bAY8l3nz
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Although there's a different fare map for every station/company, one thing that's pretty consistent is the intervals. For example, if this map were showing JR prices from Yokohama instead of Shinjuku, the closest stops would still be 140 yen, then 160, etc etc
This isn't limited to trains, either--most bus routes also have a distance-based fare (you grab a ticket while boarding, then pay when you leave, based on what the on-board electronic fare chart says you owe). Some bus routes apply a flat fare, though.
Oh, one last note: JR Fares are a bit more expensive, mile for mile, than private railway (eg Odakyu, Tokyu, etc) fares. They are still cheaper, mile for mile, than subway fares.
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