#Untested code for lack of example input by the OP
use strict; #enforces predeclaration of variables, better scoping.
use warnings; #tells you of errors or violations in your code
use Data::Dumper; #visualize your data structures

my %hash; #declaring a global variable to hold the desired column
open(my $fh, "<", "1k_genome_file.bas") or die("could not open file $!\n");
while(my $line = <$fh>){
    chomp $line;
     #split around a delimiter (a space, a tab, a comma...etc).
     my @array=split(/\t/,$line);

     #get the second column
     my $second_column=$array[1];

     $hash{$second_column}=1; 
 }
print Dumper(\%hash) #see if the hash looks like what is expected.