#! perl -slw
use strict;
use Inline::Files;

my $tally = '';
m[rs(\d{7})] and vec( $tally, $1 - 1e6, 1 ) = 1       while <FILE2>;
m[rs(\d{7})] and vec( $tally, $1 - 1e6, 1 ) and print while <FILE1>;

__DATA__
__FILE1__
chr1  11223   11224  rs2342349
chr2  23423   23424  rs6345435
chr3  64564   64565  rs3432456
chr4  56456   56457  rs7979979
__FILE2__
rs2342349
rs3274234
rs2342344