Using some modules:

use Modern::Perl '2014';
use Number::Interval;
use List::Util qw/first/;

# FILE1 data emulation
my @FILE1 = qw/99269 550 100 126477 1700/;

my @interval_objects;
while (<DATA>) {
    chomp;
    my ($start, $end, undef) = split;
    push @interval_objects,
        Number::Interval->new(
            IncMax => 0,
            IncMin => 0,
            Min    => $start,
            Max    => $end,
        );
}

for my $datapoint (@FILE1) {
    my $found = first {$_->contains($datapoint)} @interval_objects;
    say "$datapoint is in $found" if $found;
}

# FILE2 data emulation
__DATA__
517 1878 forward
700 2500 forward
2156 3289 forward
99000 100000 forward
22000 23000 backward
[download]

Output:

99269 is in (99000,100000)
550 is in (517,1878)
1700 is in (517,1878)
[download]

As said before, this will only work if the list of intervals is not huge.

It will also only find the first interval that matches. if you want to find all intervals that match, replace the for-loop by:

for my $datapoint (@FILE1) {
    my @found = grep {$_->contains($datapoint)} @interval_objects;
    say "$datapoint is in @found" if @found;
}
[download]