$chrom='chr1';
$start=9839;
$stop=9841;

while (<DATA>) {
    if (/variableStep chrom=$chrom/ ... /variableStep chrom/) {
        if (/^$start\b/ .. /^$stop\b/) {
            chomp;
            push @result, (split ' ',$_,2)[1];
        }
    }
}
use Data::Dumper;
print Dumper \@result;

__DATA__
variableStep chrom=chr1
9837    0.010
9838    0.008
9839    0.007
9840    0.004
9841    0.002
9842    0.001
variableStep chrom=chr2
9837    0.090
9838    0.038
9839    0.017
9840    0.044
9841    0.052
9842    0.091