# ll
-rwxr--r-- 1 root root  305 May 17 04:45 gen_conf.py
drwxr-xr-x 2 root root 4096 May 17 03:24 templates
-rw-r--r-- 1 root root    6 May 17 03:15 vars.csv


# cat templates/test.conf 
line 1
line 2
{% for item in items %}line {{ item }}
{% endfor %}


# cat vars.csv            
3
4
5


# cat gen_conf.py 
from jinja2 import Environment, FileSystemLoader
env = Environment(loader=FileSystemLoader('templates'))
with open('vars.csv') as vars:
    var_list = []
    for var in vars:
        var_list.append(var.strip())
template = env.get_template('test.conf')
print template.render(items=var_list)