Running this command will give you some useful information and inform you on where the default options are read from and in what order:
mysqld --verbose --help | head -15
On my system this is what it returns:
# mysqld --verbose --help | head -15
2016-06-08 11:24:30 0 [Warning] Using unique option prefix log-err instead of log_error is deprecated and will be removed in a future release. Please use the full name instead.
2016-06-08 11:24:30 0 [Note] mysqld (mysqld 5.6.24-72.2-log) starting as process 25165 ...
2016-06-08 11:24:30 25165 [Note] Plugin 'FEDERATED' is disabled.
mysqld Ver 5.6.24-72.2-log for Linux on x86_64 (Source distribution)
Copyright (c) 2009-2015 Percona LLC and/or its affiliates
Copyright (c) 2000, 2015, Oracle and/or its affiliates. All rights reserved.
Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.
Starts the MySQL database server.
Usage: mysqld [OPTIONS]
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf
The following groups are read: mysqld server mysqld-5.6
2016-06-08 11:24:30 25165 [Note] Binlog end
2016-06-08 11:24:30 25165 [Note] Shutting down plugin 'CSV'
2016-06-08 11:24:30 25165 [Note] Shutting down plugin 'MyISAM'
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