When cross-tabulating two variables, it is conventional to:

Represent the independent variable in rows and the dependent variable in columns
Assign both the dependent and independent variables to columns
Represent the dependent variable in rows and the independent variable in columns
Assign both the dependent and independent variables to rows
Represent the dependent variable in rows and the independent variable in columns  It is conventional to represent an inferred relationship between two variables in this way because it makes tables easier to read. Typically this is done when you feel you can make a claim of causality, so that a change in the independent variable produces a change in the dependent variable. Similarly, when producing a bar chart or scatter-plot, you should assign the independent variable to the x axis (to produce columns) and the dependent variable to the y axis (to produce horizontal readings).
Reference: Bryman: Social Research Methods: 5th Edition Page(s) 367,

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A. Frequencies: Percentages
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How is a variable name different from a variable label?
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