. 2013 Jan 4;34(4):885–892. doi: 10.1093/carcin/bgs407

Table IV.

Significant results of gene-based tests using three methods of PLINK set-based test, hypergeometrix and VEGAS

Gene	Chr: Position (hg18)	#			Most significant SNP		P for gene-based test
Gene	Chr: Position (hg18)	Total SNPs	Tag SNPs^a	Sig_SNPs^b	SNP ID	P value	PLINK method^c	Hypergeometric method^d	VEGAS method^c
MAFF	22:36902497..36957012	108	14	11	rs2267373	1.29E-04	5.20E-04	2.09E-10	7.50E-04
PLA2G6	22: 36837447..36907707	325	38	13	rs2012725	1.07E-04	0.006	1.27E-06	0.003
DUSP14	17: 32924063..32947701	81	20	5	rs145885981	4.64E-04	0.011	0.062	0.007
RASGRP3	2: 33514919..33643162	397	121	16	rs13391694	8.56E-04	0.011	0.012	0.013
TNFRSF1A	12: 6308184..6321544	37	13	5	rs1468603	0.006	0.013	0.012	0.011
TNF/LIST1	6: 31651328..31654091	54	26	5	rs3087617	9.39E-05	0.015	0.143	0.011
RRAS2	11: 14256041..14337305	88	17	4	rs4757245	2.28E-04	0.016	0.143	0.007
ARRB1	11: 74654129..74740521	177	50	10	rs555875	1.87E-04	0.019	0.009	0.017
DUSP2	2: 96172634..96174906	26	5	2	rs1168969	0.013	0.023	0.298	0.023
DUSP8	11: 1531856..1549726	158	13	2	rs80025267	0.002	0.028	0.866	0.023
CASP3	4: 185785843..185807623	17	12	3	rs4862396	0.007	0.030	0.276	0.022
SOS2	14: 49653595..49767849	328	24	3	rs8010248	0.003	0.035	0.792	0.031
MAPKAPK5	12: 110764661..110815611	144	6	2	rs77211491	0.008	0.035	0.392	0.013
PRKCA	17: 61729387..62237324	1374	242	22	rs1003425	5.51E-04	0.037	0.068	0.035
TGFB2	1: 216586490..216681593	40	25	5	rs1417488	0.015	0.038	0.142	0.039
STK4	20: 43028533..43142007	220	22	3	rs2284271	2.30E-04	0.039	0.726	0.011
CACNA1G	17: 45993447..46059541	195	69	10	rs2214566	0.002	0.040	0.056	0.037
DUSP4	8: 29249536..29264104	95	20	5	rs11780602	0.005	0.045	0.062	0.034
PLCB1	20: 8061295..8813547	1883	331	29	rs8123323	0.001	0.048	0.045	0.057

Sig_SNPs, significant SNPs.

^aTagSNPs were selected based on pair-wise linkage disequilibrium r² ≥ 0.8.

^bThe number of tagSNPs with significance level ≤0.05.

^cThe empirical P values were calculated 100 000 permutations/simulation using PLINK or VEGAS.

^dHypergeometric test was performed using the number of tagSNPs and significant SNPs.