#!/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;
}

##</code><code>##

0  ARRAY(0x600500ae8)
   0  empty slot   # $x starts as 1, so no element for subscript 0
   1  ARRAY(0x600500c68)
      0  'line1 file 1'
      1  'line2 file 1'
      2  ' ... etc.)
   2  ARRAY(0x600500b30)
      0  'line 1 file 2'
      2  ' ... etc.

   ... etc.

   75 ARRAY(0x6005.....)
      0  'line 1 file 75'
      2  ' ... etc.

##</code><code>##

print $id_files[$x][2];