CSS vertical align center in circles

You can use display:table property for this. Write it like this:

.SubMenu li {
  margin:50px;
  background:red;
  border-radius:50px;
  height:100px;
  width:100px;
  display:table;
}

.SubMenu a {
   height:100px;
   width:100px;
   display:table-cell;
   text-align: center;
   vertical-align: middle;
}

Check this JSFiddle.