in reply to Query large tab delimited file by a list

This will take care of the first output file quickly and easily:

#! 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

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The second output file makes no sense. The position of what in the first file? The position of what in the second? Number of matching what? Number of non-matching what?

Is that 4 lines (including all the boiler-plate text) for every line in file 1; or file 2? Or every line in file 2 that was matched? Or...

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