Are we allowed to turn down a loan if the customer is not a citizen of the US? I know we are allowed to inquire about at application, but can we turn them down for just this reason?

The Commentary to Regulation B states:

"National origin--citizenship. Under the regulation a denial of credit on the ground that an applicant is not a United States citizen is nor per se discrimination based on national origin." (See the Commentary to 202.6)

If, however, you are approving loans to Canadians, even though they're not citizens, but denying loans to Irishmen and attributing the denial to their lack of citizenship, it would appear to be impermissible discrimination on the basis of national origin because citizenship (or lack thereof) is obviously not the true differentiating factor between those applicants.