The nail holes authenticate that it was indeed Jesus who had risen from the dead. Secondly, the nail holes are a constant reminder of just how great His love is for us and they are also prophetic.

Ps 22:16

16 For dogs have surrounded me; A band of evildoers has encompassed me; They pierced my hands and my feet.
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John 19:37

37 And again another Scripture says, "They shall look on Him whom they pierced ."
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Rev 1:7

7 Behold, He is coming with the clouds, and every eye will see Him, even those who pierced Him; and all the tribes of the earth will mourn over Him. Even so. Amen.
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John 20:26-29

26 And after eight days again His disciples were inside, and Thomas with them. Jesus came, the doors having been shut, and stood in their midst, and said, "Peace be with you." 

27 Then He said to Thomas, "Reach here your finger, and see My hands ; and reach here your hand, and put it into My side; and be not unbelieving, but believing." 

28 Thomas answered and said to Him, "My Lord and my God!"

29 Jesus said to him, "Because you have seen Me, have you believed? Blessed are they who did not see, and yet believed." 
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