Table 1. CNVs enriched in T1D and Twin cohorts, relative to Ctrl.

CNP IDa	Chr	Start	End	Amplification or Deletion	Ctrl%	T1D%	Ctrl:T1D p b	Twin%	Ctrl:Twin p	Sequence
253	2p11	87,600,933	87,609,093	deletion	42	72	0.13	70	0.15	NCRNA00152
934	6p21	32,700,999	32,710,085	deletion	42	89	0.01	65	0.26	CNSc
1162	7q33	133,435,735	133,449,694	deletion	37	78	0.03	80	0.02	CNS
1303	8q11	51,194,577	51,195,974	deletion	21	61	0.03	50	0.12	SNTG1
1956	13q21	71,375,556	71,378,557	deletion	58	89	0.08	95	0.02	-

^aCNP ID as defined in McCarroll, et al. Nature Gen 40(10):1166-74.

^b p-value derived from chi-square analysis.

^cCNS =  Conserved Noncoding Sequence, defined as a region >100bp with at least 70% similarity to sequence in mus musculus (as determined by ECR browser, ecrbrowser.dcode.org).