# bedtools closest -a File1 -b File2 -d
Chr1    1000    4000    A1      Chr1    12000   18500   B1      8001
Chr1    15000   22000   A2      Chr1    12000   18500   B1      0
Chr1    30000   32000   A3      Chr1    28000   29000   B2      1001
Chr1    42000   44000   A4      Chr1    28000   29000   B2      13001