The nape. The Century D. cites Mayhew, 1851.

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1807.  Chauncy seized him by the scruff of the neck, and threw him overboard into the Boat.—Intelligencer (Lancaster, Pa.), July 28.

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1856.  ‘Varmount’ lit on him like a fierce cat, seizing him by the scruff of the neck.—San Francisco Call, Dec. 17.
  [An inquirer, Dec. 21, wishes to know what part of the human neck is called the scruff, not finding the word in Webster.]

3