Table 2.

Discovery of SNPs in the CETP Gene

	Base-specific cleavage results				Public SNPsa
Amplicon	#	Type	Positionb	Allele freq	SNP ID
Amplicon 1	1	C to T	11594/11597/11598	0.93/0.07	rs5883
	2	T to G	11690	0.85/0.15c
	3	G to A	11693/11694/11695	0.86/0.14c	rs289714
	4	G to A	11854/11855	0.47/0.53	rs158477
Amplicon 2	5	C to T	11967	0.99/0.01
	6	A to C	11978	0.46/0.54	rs158478
	7	G to A	12292	0.46/0.54	rs158479
Amplicon 3	8	G to A	12469/12471	0.13/0.87	rs158480
	9	A to G	12530/12531	0.13/0.87	rs158617
	10	A to T	12752	0.12/0.88	rs289715
Amplicon 4		T to G	13439		rs2303789d
	11	A to G	13490	0.995/0.005
Amplicon 5	12	T to A	13620	0.29/0.71	rs289716
	13	G to A	13632	0.63/0.37	rs289717
	14	T to A	14013	0.99/0.01c	rs736274
Amplicon 6	15	C to T	14176	0.30/0.70	rs289718
		T to C	14185		rs289719d
	16	T to C	14229	0.67/0.33	rs2033254
	17	G to A	14361	0.995/0.005
	18	C to T	14476	0.89/0.11
Amplicon 7	19	T to G	14626	0.92/0.08c
	20	C to T	14730	0.98/0.02
Amplicon 8	21	A to G	15072	0.68/0.32c
	22	T to G	15192	0.10/0.90	rs1968905
	23	T to G	15238	0.96/0.04
Amplicon 9	24	G to A	15429/15430	0.63/0.37
	25	G to A	15696	0.63/0.37	rs291044
Amplicon 10	26	C to T	16128/16131/16132	0.99/0.01
	27	C to T	16177/16179/16180	0.99/0.01	rs891144
		G to A	16256		rs5881d

^aThe reader is referred to http://www.ncbi.nlm.nih.gov/ for information on the public SNPs

^bPositional ambiguity was resolved by the MassEXTEND assay; the SNP position is underlined

^cThe marked allele frequencies were calculated using the Hardy-Weinberg equation; in these cases, heterozygotes could not be distinguished from either wild-type or mutant homozygous samples

^dThree public SNPs (italics) were not identified using the base-specific cleavage assay. SNPs rs2303789 (found in an Asian population) and rs5881 (allele frequency = 0.025) are absent from our sample collection. rs289719 was missed because of its genetic linkage with and close proximity to rs289718; concurrence of the two SNPs is mass-neutral