When Yosef died in Mitzraim, he was interred in Mitzraim until Moshe exhumed his remains, which were eventually brought to Israel and reinterred. However, when Reuven, Judah, etc. (the 11 brothers) died, there was no mention of their burial or exhumation. I assume they were buried in Mitzraim where they remain ad hayom hazeh. A few questions are raised: (1) Has anyone seen any information about the whereabouts of their kvarim? And related, (2) Why was their burial so low profile (these were the founders of the shvatim, quite an important role in Jewish history)?
The Sefer Hayashar (anonymous) on Sefer Yehoshua brings down where the Shevatim were buried:
שנים עשר בני יעקב אשר העלו בני ישראל ממצרים : ויקברו את ראובן ואת גד בעבר הירדן ברומיא אשר נתן להם משה לבניהם : ואת שמעון ואת לוי קברו בעיר מגדא אשר נתנה לבני שמעון ויהי מגרש העיר לבני לוי : ואת יהודה קברו בעיר בביא נגד בית לחם : ואת עצמות יששכר וזבולון קברו אותם בצידון בחלק אשר נפל לבניהם : ודן נקבר בעיר בניו באשתאול : ואת נפתלי ואת אשר קברו אותם בקדש נפתלי איש איש במקומו אשר ניתן לבניו : ואת עצמות יוסף קברו בשכם בחלקת השדה אשר קנה יעקב מאת חמור ויהיו לבני יוסף לנחלה : ואת בנימן קברו בירושלם נגד היבוסי אשר נתן לבני בנימן : איש בעיר
And Joshua cut a covenant with the people on that day, and he sent the children of Israel away and they went each one to his inheritance and to his city. And it came to pass in those days, when the children of Israel dwelt securely in their cities, that they buried the coffins of the fathers of their tribes, which they had brought up with them from Egypt, every one of the twelve sons of Jacob was buried by the children of Israel in the inheritance of his children. And these are the names of the cities wherein the twelve sons of Jacob were buried, whom the children of Israel had brought up from Egypt. And they buried Reuben and Gad on this side of the Jordan, in Rumia, which Moses had given unto their children. And Simeon and Levi they buried in the city of Manda which was given unto the children of Simeon, of which a certain part had been assigned for the sons of Levi. And Judah they buried in the city of Benjamin opposite Beth-lehem. And the bones of Issachar and Zebulun they buried in Zidon, in the portion which had fallen to the lot of their children, and Dan was buried in the city of his children the city of Eshtael. And Naphtali and Asher they buried in Kadesh-Naphtali, each one in the place given unto his children. And the bones of Joseph they buried in Shechem, in the portion of the field which Jacob had bought from Hamor, and which became the inheritance of the children of Joseph. And Benjamin they buried in Jerusalem, opposite the Jebusite, which was given unto the children of Benjamin; thus the children of Israel buried their ancestors, everyone in the city of his children.