No need for a hash, an array should be enough. Try the following: 
#!/usr/bin/perl
use warnings;
use strict;

open my $GENES,     '<', 'genes'     or die $!;
open my $LOCATIONS, '<', 'locations' or die $!;

chomp(my @locations = map { (split ' ')[1] } <$LOCATIONS>);
# If IDs are not already sorted, uncomment the following line:
# @locations = sort { $a <=> $b } @locations;

for (<$GENES>) {
    my ($chromosome, $start, $end) = split ' ';
    print "$chromosome\t$start\t$end";
    my $idx = 0;        # For $end, start searching where you left for
+ $start.
    my $correction = 0; # Needed for Start(-) == Start and End(+) == E
+nd.
    for my $pos ($start, $end) {
        $idx++ while $locations[$idx] <= $pos - $correction
                     and $idx <= $#locations;
        die "No numbers around $pos ($idx)\n"
            if $idx == 0 or $idx > $#locations;
        print "\t$locations[$idx-1]\t$locations[$idx]";
        $correction = 1;
    }
    print "\n";
}

[download]
Update: Fixed border cases.
لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: Reading values from one .csv, searching for closest values in second .csv, returning results in third .csv? by choroba
in thread Reading values from one .csv, searching for closest values in second .csv, returning results in third .csv? by pickleswarlz

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