Several questions linked in the FAQ could answer parts of this question, or at least give a background on why Jews were persecuted.

https://www.reddit.com/r/AskHistorians/wiki/faq/religion#wiki_judaism

For example by /u/VetMichael here or this answer by /u/yodatsracist here

As for physical traits most of these came from depictions of Jews in art.

The first sign of a Jewish trait was a pointy hat, when Christians began to look at “Old Testament” they made art of Jews wearing a Phygrian cap.. This was assumed to be how Jews dressed, it comes from a cap worn (possibly) worn by some Babylonian Jews. The same cap appears on depictions of “The Three Magi”. Some wore a similar cal in the middle ages, after the Fourth Council of the Lateran (1215) the hat was required to be worn by Jews when not in the ghetto to identify themselves.

The Nose was first shown in 1170 in a painting: Jesus nailed to the cross under the direction of Jewish and Gentile executioners, enamel reliquary casket, circa 1170

The Jew in the picture (second from left) has a large hook nose which is out of proportion to the face. How,ever at this time their is no record of it being associated with stereotypes. As artwork changed to portraying Christ dying on the cross this nose would show up again and again as a way to stress Jews uncaring nature about the cruxifixction and as a clear visible sign they ate turned away.

In the late 13th century realism in art became the ideal and a standard physiology was set for portrayal of Jews in artworks. At this time the stereotypical image of Jews was born. An illustration of Psalm 52, “The fool says in his heart, ‘There is no God,’” a detail from the Psalter and Hours of Bonne of Luxembourg, circa 1340

Books: Sarah Lipton Dark Mirror: The Medieval Origins of Anti-Jewish Iconography