In the Miqraot Gedolot, an index exists called Toldot uVeit Aharon. It lists "every" passage in the early rabbinic literature that references every individual passuk, and is extremely useful. Another, more fuller, version of the same is the three-volume Torah haKetuvah vehaMesorah. Does anybody know if a similar index exists for the Mishna? I would love to be able to know where any individual mishna is referenced throughout the Bavli and the Yerushalmi.
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There's one, with a title atop the column that reads "ציונים", in the outside margin of the standard-print mishnayos (the one with the Yachin Uvoaz).