if first line of file2 is a primary key, below will work. But if not, it will fail like this ... 
use strict;
use warnings;

my $file1=<<EOF;
23 SNP_A-4293670 0 2713391
24 SNP_A-4293670 0 2713391
25 SNP_A-1780270 0 1111111
26 SNP_A-1780271 0 2222222
EOF

my $file2=<<EOF;
SNP_A-1780270 ss75925050 rs987435
SNP_A-1780271 ss75925050 rs000001
SNP_A-4293670 ss75925050 rs999999
SNP_A-4293670 ss75925050 xxxxxxxx
EOF

my %lookup;
foreach my $line ( split( /\n/, $file2) ){
    my @line=split(/\s+/,$line);
    $lookup{$line[0]}=$line[2];
}
print "k=$_,v=$lookup{$_}\n" for keys %lookup;

foreach my $line ( split( /\n/, $file1) ){
    my @line=split(/\s+/,$line);
    printf "%s\t%s\t%s\t%s\n", $line[0], $lookup{$line[1]}, $line[2], 
+$line[3];
}

[download]

result 

23      xxxxxxxx        0       2713391
24      xxxxxxxx        0       2713391
25      rs987435        0       1111111
26      rs000001        0       2222222

[download]
first column of the seconde file is the problem. Is it unique key?

In reply to Re: Replace data in the column of one file with corresponding ones in another file by remiah
in thread Replace data in the column of one file with corresponding ones in another file by Renyulb28

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