It was always a point made from very early times that Rome was the church of Peter. As opposed to places like Alexandria for example whose status came from it being the see of a disciple of Peter.
Something else I seem to recall is that one of the leg bones was different -- what would be expected from a Galilean fisherman always putting one leg on the side of a boat to haul in a fishing net.
The final resting place of a number of Apostles is more or less known -- Ss Simon and Jude are in Saint Peter's, Saint Paul is buried in Saint Paul Outside the Walls in Rome, Saint James the Greater is at Compostella in Spain, Saint Bartholomew is in a church on an island in the Tiber in Rome, Saints Philip and James the Lesser have their own church in Rome I think.