Systematic search for enhancer elements and somatic allelic imbalance at seven low-penetrance colorectal cancer predisposition loci

Table 1 Genotyping of 12 SNPS that locate in transcription factor binding sites in low-penetrance CRC loci

Locus	SNP bp*	SNP ID	MAF controls	MAF cases	OR	95% CI	P	Cases (n)	Controls (n)	Binding sequence***	TF
15q13	30 782 048	rs4779584**	0.295	0.323	1.14	1.00 - 1.31	0.05	981	1 024
	30 806 855	rs28768389	0.088	0.073	1.24	0.97-1.57	0.08	976	837	AAYCAATCACATA	GATA2-FOXL1
	30 824 927	rs11631292	0.123	0.108	1.16	0.95-1.42	0.15	1 009	823	YATCC	GATA2
	30 825 051	rs62002613	monomorphic					1 011	824	KATCT	GATA2
	30 806 691	rs12899808	monomorphic					976	837	MCAACAT	BRCA1
	30 804 840	rs34812868	0.431	0.402	1.13	0.99-1.29	0.08	913	821	GTRTCT	GATA1
10p14	8 741 225	rs10795668**	0.307	0.271	1.19	1.04-1.37	0.01	951	983
	8 743 013	rs17485426	0.129	0.137	1.07	0.88-1.29	0.51	1 010	824	TATMTAAA	FOXL1
	8 742 714	ENSSNP10169878	0.129	0.137	1.07	0.88-1.29	0.51	1 010	824	CAATCTTAWTTTTT	GATA3-FOXC1
	8 783 743	rs1999638	0.123	0.136	1.12	0.92-1.37	0.24	1 010	824	RAATCT	GATA3
11q23	110 676 919	rs3802842**	0.239	0.276	1.22	1.06-1.40	0.01	970	994
	110 645 918	rs12273224	monomorphic					997	823	TAAATRTA	FOXL1
	110 669 934	rs45615536	0.01	0.006	1.63	0.77-3.57	0.19	1 009	824	TKGGGG	MZF1
14q22	53 480 669	rs4444235**	0.426	0.462	1.16	1.02-1.33	0.03	933	828
	53 488 736	rs2761880	0.009	0.008	1.08	0.51-2.23	0.85	1 011	824	GTGTTTYTTTATTCTT	FOXJ3
	53 484 488	rs12893484	0.384	0.414	1.13	0.99-1.29	0.07	1 010	824	GCCRCAGGC	TFAP2A

* Human genome build 36; **Tag SNPs genotyped in previous studies [6, 8, 9]; *** SNPs indicated as Y = C/T, K = G/T, M = A/C, R = A/G, W = A/T; MAF = minor allele frequency, TF = transcription factor; rs11631292, rs62002613, rs17485426, ENSSNP10169878, rs1999638, rs12273224, rs45615536, rs10505287, rs57897735 rs10505283, rs2761880, and rs12893484 were genotyped using Sequenom MassArray iPlex Gold; rs28768389, rs12899808, and rs34812868 were genotyped using genomic sequencing

ISSN: 1471-2350