Here are a couple of other alternatives.
Data Transfer Tool - You can run the iSeries Data Transfer Tool from the command line (RTOPCB). First, run the GUI version and create a definition file. If you edit this file with a text editor, you will see that this is just an old-fashioned INI file and you can easily find the line with the query in it. From there, you could write a batch file or otherwise pre-process the text file to allow you to manipulate the query before submitting it to the query tool.
QSHELL - If you can log on to the iSeries interactively, then you may find the QSHELL environment more familiar than CL or REXX (although REXX is kind of fun). QSHELL is a full POSIX environment running on the iSeries. Use the command STRQSH to start QSHELL. You can have ksh or csh as a shell. Inside QSHELL, there is a command called "db2" that submits queries. So, you should be able to do something like this inside QSHELL:
system> VariableName = 'blah blah'
system> db2 "select * from TableName where Column = \'$VariableName\'"
You may have to fiddle with the quotes to get ksh to pass them correctly.
Also, inside QSHELL, you should have a full Perl installation that will allow you to use DBI to get data.
Some other ways to interact with data on the iSeries: query from the client with Python via ODBC; query from the client with Jython via JDBC; install Jython directly on the iSeries and then query via JDBC.