. Author manuscript; available in PMC: 2008 Apr 28.

Published in final edited form as: Carcinogenesis. 2008 Jan 3;29(2):333–341. doi: 10.1093/carcin/bgm284

Table III. Haplotype analysis of all tag SNPs genotyped in set 1.

Gene^a	Haplotype	Frequency	P-value	OR	95% CI
CCND1	h1010000	0.343	0.256
07, 02, 03, 08, 10, 04, 01	h0001110	0.296	0.038	1.105	1.006–1.214
	h0001100	0.098	0.163
	h0000000	0.085	0.166
	h1010001	0.070	0.629
	Combined rare^b		0.102
CCND2	h100000	0.3496	0.636
Block 1—03, 09, 10, 11, 05, 18	h010001	0.2203	0.198
	h001010	0.1536	0.274
	h000011	0.1113	0.467
	Combined rare		0.698
CCND2	h000100	0.3653	0.740
Block 2—14, 15, 16, 06, 17, 07	h011001	0.2276	0.752
	h100010	0.1925	0.272
	Combined rare^b		0.239
	h000010	0.0443	0.050	1.234	1.000–1.523
CCND3	h0011100	0.2515	0.211
08, 07, 06, 03, 02, 04, 01	h0000001	0.2499	0.482
	h0100000	0.2352	0.221
	h1001010	0.1640	0.544
	Combined rare^b		0.731
	h0000000	0.0362	0.048	1.254	1.002–1.568
CCNE1	h0000	0.3353	0.169
02, 12, 05, 08	h1100	0.3211	0.187
	h0001	0.2291	0.719
	h1000	0.0763	0.479
	Combined rare^b		0.990
CDK2	h00	0.6091	0.806
02, 04	h10	0.3078	0.903
	h01	0.0601	0.858
	Combined rare^b		0.847
CDK4	h10	0.4318	0.209
01, 02	h01	0.3319	0.225
	h00	0.2352	0.929
	Combined rare^b		0.796
CDK6	h000001	0.4634	0.552
Block 1—09, 12, 08, 11,13, 01	h101000	0.2041	0.304
	h010010	0.0965	0.034	0.860	0.748–0.989
	h010000	0.0921	0.654
	h001000	0.0629	0.676
	h010100	0.0554	0.142
	Combined rare^b		0.741
CDK6	h000	0.5303	0.662
Block 2—02, 03, 10	h010	0.2818	0.253
	h110	0.0969	0.167
	h011	0.0883	0.024	0.843	0.726–0.978
	Combined rare^b		0.239
CDK6	h0000	0.5197	0.708
Block 3—04, 05, 06, 07	h0100	0.2049	0.754
	h0010	0.1037	0.742
	h0001	0.0789	0.893
	h1001	0.0602	0.480
	Combined rare^b		0.824
CDKN1A	h0000	0.5874	0.198
Block 1—07, 06, 17, 11	h1110	0.2055	0.635
	h0101	0.1279	0.954
	h1100	0.0551	0.346
	Combined rare^b		0.092
CDKN1A	h0000	0.5690	0.063
Block 2—12, 14, 01, 02	h1001	0.1708	0.454
	h1000	0.1609	0.948
	h1111	0.0502	0.289
	Combined rare^b		0.047	1.238	1.003–1.529
CDKN1A	h00	0.8418	0.014	0.864	0.769–0.971
Block 3—03, 04	h01	0.0942	0.182
	h10	0.0587	0.050	1.199	1.000–1.438
	Combined rare^b		0.361
CDKN1B	h10000000	0.2731	0.552
04, 05, 01, 02, 06, 07, 03, 08	h01001010	0.0927	0.186
	h00100010	0.0840	0.218
	h10010000	0.0816	0.356
	h00101010	0.0611	0.338
	h00100000	0.0576	0.323
	h00000001	0.0571	0.448
	Combined rare^b		0.557
CDKN2A2B	h1000000001010010	0.1943	0.192
CDKN2A—13, 11, 10, 12, 09,	h0000100000000001	0.1682	0.724
14, 01, 02, 15, 03, 04;	h0000100000001001	0.1161	0.994
CDKN2B-04, CDKN2B-03,	h0000001110000001	0.0911	0.886
CDKN2A-05, 06, CDKN2B-02	h0100010010010000	0.0828	0.175
	h0010000110100100	0.0660	0.741
	Combined rare^b		0.120
CDKN2C	h00	0.5685	0.857
02, 01	h10	0.3360	0.454
	h01	0.0950	0.130
	Combined rare^b		0.915
CDKN2D	h00	0.7629	0.331
02, 01	h10	0.1865	0.289
	h11	0.0502	0.954
	Combined rare^b		0.601

SNPs used for haplotype analysis are arranged in chromosome order.

Rare haplotypes (<5%) were pooled.