Manchu dynasty, name given to naturalized foreigners
秦 centers on the historical Qin dynasty of China, and by extension came to be used as a name for naturalized foreigners in Japan, likely reflecting the dynasty's cultural influence.
秦 is the name of the Qin dynasty, and its character form is historically associated with the region. The modern shape visually contains 禾 (grain) below a top element, but the exact historical development of the components is uncertain.
The top part looks like three people (三 and 人) standing over a grain plant 禾, as if representing the people of the Qin dynasty working the fields.
For シン, imagine the Qin dynasty's first emperor, Qin Shi Huang, whose name starts with 'Shin' in Japanese: Shin -> シン.