use strict;
use warnings;

my ( $file1, $file2 ) = ( 'file1_name_here', 'file2_name_here' );

# read hash keys and values from file1:

open( F, '<', $file1 ) or die "$file1: $!\n";
my %mods;
while (<F>) {
    chomp;
    my ( $key, $val ) = ( split /\t/ )[0,4];
    $mods{$key} = $val;
}
close F;

# read and rewrite file2, altering certain lines as needed

open( IN, '<', $file2 ) or die "$file2: $!\n";
open( OUT, '>', "$file2.new" ) or die "$file2.new: $!\n";
while (<IN>) {
    chomp;
    my ( $loc, $chk ) = ( split /\t/ )[0,11];  # or should it be [0,10]?

    if ( $loc =~ /location/ ) {   # modify some input lines as needed
        $_ .= "\t YRI_iHs\n";
    }
    elsif ( exists( $mods{$chk} )) {
        $_ .= "\t$mods{$chk}\n";
    }

    print OUT;  # print every input line to output file
}
close IN;
close OUT;

# you could rename the output to replace the original...
# rename "$file2.new", $file2; 
# (but you might want to check the output first)