You could turn the problem inside out: load the test values into memory then scan the large reference file one line at a time to perform the matching:

#!/usr/bin/perl

use strict;

my $reps = <<REPS;
chr1 100 120 feature1
chr1 200 250 feature2
chr2 150 200 feature1
chr2 280 350 feature1
chr3 100 150 feature2
chr3 300 450 feature2
REPS

my %tests;
while (my $line = <DATA>) {
    $line =~ s/[\n\r]//g;
    my @array = split /\s+/, $line;
    $tests{$array[0]}{$array[1]}{'end'} = $array[2];
    $tests{$array[0]}{$array[1]}{'rep'} = $array[3];
}

open my $repIn, '<', \$reps;

while (<$repIn>) {
    my ($chr, $start, $end, $rep) = split ' ';

    next if !exists $tests{$chr};

    for my $s (keys %{$tests{$chr}}) {
        if ($start <= $tests{$chr}{$s}{'end'}) {
            last if $s >= $end;
            print "$chr $start $end $rep\n";
        }
    }
}

__DATA__
chr2 160 210
[download]