Table 2. CNVs depleted 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
1102	7q11	66,266,764	66,282,667	deletion	68	39	0.14	10	0.001	TYW1
1879	12q23	98,319,424	98,322,865	deletion	47	22	0.20	10	0.02	ANKS1B
A588c	15q11	18,491,920	19,803,369	both	58	33	0.24	10	0.004	BCL8, POTEB, GOLGA6L6, GOLGA8C
2240	17p12	15,483,886	15,487,515	deletion	42	22	0.35	0	0.004	TRIM16

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

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

^cA588 is a novel variant identified in this study.