Typical schema

suggest change
CREATE TABLE XtoY (
    # No surrogate id for this table
    x_id MEDIUMINT UNSIGNED NOT NULL,   -- For JOINing to one table
    y_id MEDIUMINT UNSIGNED NOT NULL,   -- For JOINing to the other table
    # Include other fields specific to the 'relation'
    PRIMARY KEY(x_id, y_id),            -- When starting with X
    INDEX      (y_id, x_id)             -- When starting with Y
) ENGINE=InnoDB;

(See Remarks, below, for rationale.)

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