Table 5.

Breakpoint regions identified by SNP-array analysis of the 46,XY,der(12)dir ins(12;9)(q23;p21p23)mat case

Breakpointa	Chromosome band	Defining SNP		Disrupted gene	Breakpoint in gene	Histone modificationb	DNAse I hypersensitivity	CpG island	DNA methylation sites	Transcription factor binding sites	Replication timingc
		left	right
1		rs4740872	rs7860449	KDM4C	intron 17	no	no	no	no	no	S3-S4
2		rs946452	rs1339284	no	no	no	Strong	no	no	no	S4-G2
3	9p23	rs11790910	rs11793993	MPDZ	intron 3	no	no	no	no	GATA3	S1-S2
4	9p23	rs7038314	rs7863476	PLAA	exon 14	no	no	no	no	no	S1-S2
5	9p23	rs10120052	rs13285154	no	no	no	no	no	no	no	S3-S4
6	9p23	rs2295797	rs3763630	TLN1	intron 1	H3K27ac	Strong	no	no	CTCF, RFX5, NFYB, POLR2A	G1b
7	12q23.1	rs11615348	rs10777975	ANKS1B	intron 12	no	no	no	no	no	S4-G2
8	12q23.1	rs10860431	rs7301622	ANKS1B	intron 11	no	no	no	no	MAFK	S4-G2
9	12q23.2	rs7965233	rs1007916	no	no	no	no	no	no	no	S3-S4
10	12q23.2	rs11111423	rs4764936	no	no	no	no	no	no	no	S4-G2

^aRefers to the deletion regions shown in figure 3.

^bH3K27ac mark is often found near regulatory elements.

^cReplication timing data according to Hansen et al. [2010]. SNPs in bold are diploid, italicized are duplicated and SNPs in normal font are deleted. Genes, motives or sites of interest within 1 kbp of the breakpoint regions [de Pater et al., 2002].