#!/usr/bin/perl
use strict;
use warnings;

my $CHR_NUM = $ARGV[0];

my $file_location = "/home/ALL.chr$CHR_NUM.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz";

my @id_files;           # you might find a better variable name for that array of arrays
for my $x (1..75) {     # $x is a poor name for a variable, perhaps $file_nr would be better
        my $file_in = "/home/raj/HAPLOTYPES_JAN_2015/PROG_1_Approach_2/C22-$x";
        open my $FH, $file_in or die "Cannot open $file_in $!"; # if one fails, you might be happy to know which one of the 75 files
        while (my $line = <$FH>){
                chomp $line;
                push @{$id_files[$x]}, $line;
        }
        close $FH;
}