According to some dictionary, "じゃ"(ja) is a sound change or a contraction of "では"(dewa).

Using ja(じゃ) is an informal way of dewa(では). 

じゃない(jya nai)               　　　　→　most informal

ではない(dewa nai) 

じゃありません(jya arimasenn)  

ではありません(dewa arimasenn)　→　most formal

They both mean "be not", but dewa arimasen is formal way more than ja arimasen.

Actually people use both in conversation in formal or casual in Japan.

Dewa arimasen sounds elegant for me.