This is the true story of Anne Frank, a Jewish girl living in Amsterdam during WW2. Anne's father realizes on time the danger the Jews face and hides his family (his wife Edith and his two daughters Margo (16) and Anne (13), along with four more people, in "the house behind". For two years the 8 people live in darkness and whispers, in fear to be discovered and sent to the German crematories. During that time young Anne writes a diary, describing day by day life in the cellar, her complicated realtionship with her mother and the story of her first love - Peter, the young boy in the hiding place. Anne writes down her wishes to run out free and breath the air and flowers, her dreams to be free at last. Then they are discovered and are all sent to death.
The Jewish population in Japan may be tiny (IT'S UNDER 9000!), but there's a long history of exchange between Jewish and Japanese culture. Here's some historical background and a list of stand-out Jewish characters in anime, manga, and light novels.