Yeah, ジーン is an onomatopoeia for the state of "(your hands/legs etc.) being numb", but ジーンとする (or ジーンと来る) normally means "to be emotionally touched, moved". cf. 感動する/感激する. 「じーんとする」in Weblio-dictionary:　http://thesaurus.weblio.jp/content/%E3%81%98%E3%83%BC%E3%82%93%E3%81%A8%E3%81%99%E3%82%8B

It means "extremely cold feeling that makes one feel numb;sharp pain that is almost numbing" I kinda feel it right now while typing :)