Intersecting two different files with one "master" file based on different columns
An awk solution

awk '
    FILENAME == ARGV[1] {f2[$2] = $2 OFS $3 OFS $4 OFS $5 OFS $6 OFS $7; next}
    FILENAME == ARGV[2] {f3[$2] = $2 OFS $3 OFS $4 OFS $5 OFS $6 OFS $7; next}
    {
        for (key2 in f2) {
            for (key3 in f3) {
                if (($2 &lt;= key2 &amp;&amp; key2 &lt;= $3) &amp;&amp; ($5 &lt;= key3 &amp;&amp; key3 &lt;= $6)) {
                    print $1,$2,$3,$4, f2[key2], $5,$6,$7, f3[key3]
                }
            }
        }
    }
' file2 file3 file1


outputs

1 15776220 15776240 GTGACCAGCAGGTGTCTCTG 15776231 2 5008 G:5002 A:6  16855676 16855696 CTGTCCAGCAGAGGGCGGTG 16855677 2 5008 A:5003 C:5
1 15776220 15776240 GTGACCAGCAGGTGTCTCTG 15776231 2 5008 G:5002 A:6  16855676 16855696 CTGTCCAGCAGAGGGCGGTG 16855689 3 5008 G:4957 A:41 T:10
1 15776220 15776240 GTGACCAGCAGGTGTCTCTG 15776239 3 5008 C:3358 A:14 G:1636 16855676 16855696 CTGTCCAGCAGAGGGCGGTG 16855677 2 5008 A:5003 C:5
1 15776220 15776240 GTGACCAGCAGGTGTCTCTG 15776239 3 5008 C:3358 A:14 G:1636 16855676 16855696 CTGTCCAGCAGAGGGCGGTG 16855689 3 5008 G:4957 A:41 T:10


For your sample data, all combinations of records in file2 and file3 meet the criteria for the file1 record.