$ cat 1.txt
chr1 14765298 14766727 def
chr1 16759093 16760238 def
chr1 16759236 16760238 def
chr1 20782516 20784428 him
chr1 20989962 20991078 her
chr2 31672150 31673532 abc
chr2 33157721 33158124 abc
chr3 34542283 34542962 abc
chr3 38248682 38251416 abc
chr4 58562053 58567653 abc
$ cat 2.txt
chr1 21438731 21439423 26.12
chr1 33939851 33940673 34.76
chr1 36779864 36780494 20.16
chr1 36817091 36817917 27.22
chr2 36977015 36977908 19.27
chr3 40475125 40475885 21.58
chr3 40483838 40484616 15.3
chr4 40502827 40503675 10.61
chr4 40532299 40533156 14.78
chr5 43593022 43594143 24.33
$ cat script.awk
BEGIN {
        if ( ARGC != 3 ) {
                print "Usage: awk -f script.awk <file1> <file2>"
                exit 0
        }
}

FNR == NR {
        f1_data[ FNR ] = $0
        next
}

FNR < NR {
        for ( i = 1; i <= length( f1_data ); i++ ) {
                split( f1_data[ i ], fields )
                if ( fields[1] != $1 ) {
                        next
                }
                substraction = fields[2] - $2
                if (substraction >= -1000000 && substraction <= 1000000 ) {
                        for ( j = 2; j <= length( fields ); j++ ) {
                                f1_line = (f1_line ? f1_line " " : "" ) fields[j]
                        }
                        printf "%s %s %d\n", $0, f1_line, substraction
                        f1_line = ""
                }
        }
}
$ awk -f script.awk 1.txt 2.txt 
chr1 21438731 21439423 26.12 20782516 20784428 him -656215
chr1 21438731 21439423 26.12 20989962 20991078 her -448769