Table 4. All CNVs greater than 2 Mb.

Chr	start	end	SNPs	length	state	start SNP	end SNP	Status	Cohort	Notes
1	144106312	146293282	260	2,186,971	del	rs10797649	rs2932454	case	Aberdeen	This deletion has been found in other schizophrenia samples [22],[24]. A 1.4 Mb deletion was also found in the US cohort at the same location (chr1:144838594–146293282).
1	144106312	146292286	259	2,185,975	del	rs10797649	rs2999617	case	Aberdeen
8	15098795	18360001	536	3,261,207	del	rs12680924	rs7000897	case	Munich	Includes TUSC3, associated with mental retardation [47] , PCM1, which has been associated with schizophrenia [48] , ASAH1, whose deficiency results in mental retardation [49] and NAT1 and NAT2 which have been implicated in schizophrenia.
16	15387380	18072544	491	2,685,165	del	rs251633	rs9284326	case	Aberdeen	Includes NDE1, which interacts with DISC1 to control neurodevelopmental processes [25] , [34] .
22	16389909	19792353	668	3,402,445	del	rs174330	rs140392	case	Aberdeen	Region implicated in schizophrenia in multiple studies.
22	17257787	19792353	496	2,534,567	del	rs2543958	rs140392	case	Aberdeen
22	17257787	19792353	496	2,534,567	del	rs2543958	rs140392	case	Aberdeen
22	17257787	19792353	496	2,534,567	del	rs2543958	rs140392	case	Aberdeen
1	185089907	187703805	220	2,613,899	dup	rs2076075	rs3860306	case	Munich	PLA2G4A is the only gene affected by this event. This gene has previously been implicated in schizophrenia [63].
2	106190084	109173575*	455	2,983,492	dup	rs13006272	rs11893469	case	Aberdeen	Includes many genes, none previously implicated in schizophrenia.
4	96866611	99167973	156	2,301,363	dup	rs2865703	rs783919	case	Munich	PDHA2 in region, not good candidate gene.
4	179888441	182314469**	567	2,426,029	dup	rs436324	rs12503294	control	US	No genes in region
5	37621606	39730156	490	2,108,551	dup	rs665327	rs1499238	control	Aberdeen	Includes many genes, including good schizophrenia candidates, e.g. GDNF. However subject is unaffected.
13	79334893	81402686	381	2,067,794	dup	rs6563141	rs9531267	case	Aberdeen	Includes SPRY2, which shows decreased expression in brains of schizophrenia patients[64].
15	21240037	26208861	556	4,968,825	dup	rs4778531	rs1635168	case	Munich	Includes many genes, notably GABRA3 and GABRA5, overlaps with larger duplication found in US cohort.
15	21260328	30302218***	1600	9,041,890	dup	rs17118751	rs4779984	case	US	Overlaps both with duplication in Munich cohort and also region of previously reported schizophrenia-associated 1.4 Mb duplication encompassing APBA2 [40].
22	17343340	19792353	347	2,449,014	dup	rs2019061	rs140392	control	Munich	Same region deleted in cases. A 1.5 Mb duplication was also seen in a US case (chr22:17257787–18719310)

*: Inspection in BeadStudio indicates that this duplication is actually 4.06 Mb, extending from chr2: 106282170–110339905.

**: Inspection in BeadStudio indicates that this duplication is actually 2.91 Mb, extending to chr4: 182,802,687.

***: Inspection in BeadStudio indicates that this duplication is actually 9.41 Mb, extending to chr15: 30,544,756.