You can issue the following query from the command line:
mysql -uUSER -p -e 'SHOW VARIABLES WHERE Variable_Name LIKE "%dir"'
Output (on Linux):
+---------------------------+----------------------------+
| Variable_name | Value |
+---------------------------+----------------------------+
| basedir | /usr |
| character_sets_dir | /usr/share/mysql/charsets/ |
| datadir | /var/lib/mysql/ |
| innodb_data_home_dir | |
| innodb_log_group_home_dir | ./ |
| lc_messages_dir | /usr/share/mysql/ |
| plugin_dir | /usr/lib/mysql/plugin/ |
| slave_load_tmpdir | /tmp |
| tmpdir | /tmp |
+---------------------------+----------------------------+
Or if you want only the data dir use:
mysql -uUSER -p -e 'SHOW VARIABLES WHERE Variable_Name = "datadir"'
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