The classification variables X2-X12 do not appear in the model because you have not listed them on the MODEL statement. It sounds like you want:
MODEL Y = X1-X12 / link=genlogit;
As to the Y variable, each nonreference value of that variable get a separate set of parameter estimates. In the parameter estimates table you will see an intercept for Y=1, Y=2, etc. Similarly, a coefficient for X1 for Y=1, Y=2, etc.
Look at the output for this example and notice the second column displays the levels of Y to which the estimates are associated:
data Have;
call streaminit(123);
do i = 1 to 100;
x1 = rand("Normal");
y = rand("table", 0.3, 0.4, 0.2, 0.1);
output;
end;
run;
proc logistic data=Have;
class Y (ref="3") /param=ref;
model Y = X1 / link =genlogit;
run;