Referee 2's Review:
This is an interesting and hypothesis generating study utilizing a large cohort of patients. Please address the following queries
1) Methods: you state that DNA was de-identified but also that subjects were consented and then samples obtained. Were they given a unique study # or truly deidentified
2) how were controls selected?
3) is there more information, particularly in the male cohort on the diagnostic criteria met for diagnosing SLE. Specifically, do these polymorphisms associate more with certain manifestations of SLE? (leukopenia, etc etc)
4) would state in the conclusions that, as with all SNP studies, no matter how large, validation in a second cohort is needed
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N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.
