T-Trees

A novel tree-based approach for Genome-Wide Association Studies

Supplementary data

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2	Best: rs6733115 (2)	Gene	217.31-217.34Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6733115		217314460	0.001628	1	1	8.627e-06	0.00047	59
	rs9341144		217336160	0.008857	1	1	3.642e-06	9.8e-05	200
3	Best: rs12163649 (3)	Gene	150.14-150.16Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12163649		150135318	0.2494	0.07213	0.04861	0.002901	0.0002	95
	rs6807987		150162594	0.2711	0.7011	0.113	0.0002955	0.0001	192
	rs6440578		150164401	0.2748	0.2535	0.2171	0.0002938	0.00014	140
3	Best: rs10513440 (2)	Gene	154.52-154.52Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7612570		154515875	0.1709	0.9389	8.019e-05	0.05559	0.00011	181
	rs10513440		154523522	0.1966	0.1696	0.002705	0.01709	0.00016	116
6	Best: rs2610769 (2)	Gene	89.37-89.38Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2610769		89374315	0.1484	0.1701	0.002686	0.0726	0.00013	147
	rs2756368	RNGTT NCBI Gene Pubmed Genecard	89382364	0.1455	0.08161	0.01195	0.07997	0.0001	196
6	Best: rs2757045 (2)	Gene	167.32-167.32Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2757045	RNASET2 NCBI Gene Pubmed Genecard	167321374	0.1025	0.00613	0.2912	0.01328	0.00024	82
	rs2757048	RNASET2 NCBI Gene Pubmed Genecard	167321531	0.1014	0.008134	0.2412	0.01284	0.00022	85
7	Best: rs2519602 (2)	Gene	93.00-93.01Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2677056		93004682	0.1506	0.01839	0.1186	0.0247	0.00013	150
	rs2519602		93008050	0.1492	0.006595	0.1552	0.03263	0.00013	149
9	Best: rs488101 (5)	Gene	117.69-117.81Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11793751		117693568	0.1411	0.1101	0.3654	0.8131	0.00024	78
	rs2458879		117783588	0.3856	0.388	0.847	0.4464	0.00022	86
	rs488101		117787179	0.3633	5.561e-06	0.5866	4.696e-07	0.00056	52
	rs2151370		117804641	0.3789	0.8846	0.7863	0.2109	0.00024	81
	rs2780244		117808231	0.3812	0.6991	0.5872	0.2695	0.00013	156
10	Best: rs3122348 (9)	Gene	30.99-31.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	SNP_A-2100739		30990735	0.08045	0.2412	0.7978	0.241	0.017	4
	rs3122348	LOC645954 NCBI Gene Pubmed Genecard	30991151	0.03374	4.725e-06	1	6.122e-96	0.13	1
	rs7078126	LOC645954 NCBI Gene Pubmed Genecard	31024312	0.07923	0.7591	1	0.849	0.011	8
	rs7093972	LOC645954 NCBI Gene Pubmed Genecard	31024349	0.07818	0.6394	0.523	0.8782	0.01	9
	rs16930258	LOC645954 NCBI Gene Pubmed Genecard	31037513	0.08511	0.1682	0.2567	0.1612	0.0003	66
	rs7910154	LOC645954 NCBI Gene Pubmed Genecard	31040399	0.1357	0.6948	0.5372	0.4891	0.00061	49
	rs10763821	LOC645954 NCBI Gene Pubmed Genecard	31040907	0.1372	0.5571	0.4444	0.419	0.00065	47
	rs3858241	LOC645954 NCBI Gene Pubmed Genecard	31041299	0.06603	1	0.02188	0.5615	0.0089	12
	rs1494134		31057878	0.1468	0.463	0.4684	0.5415	0.0013	33
10	Best: rs2393191 (2)	Gene	58.39-58.41Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2393191		58394623	0.01562	0.3097	0.571	0.2463	0.0026	21
	rs16909905		58410545	0.01198	1	0.3529	0.9247	0.0026	22
10	Best: rs7080464 (3)	Gene	131.95-132.00Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11017171		131947751	0.05863	0.03355	0.1852	0.7923	0.00013	154
	rs7080464		131974739	0.03085	0.04696	0.4053	5.071e-08	0.0013	32
	rs7918047		132001099	0.05836	0.09054	0.4042	0.8607	0.0002	92
11	Best: rs493888 (2)	Gene	133.33-133.34Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs561561		133334916	0.1185	1.177e-05	0.7288	0.4834	0.00017	103
	rs493888		133337683	0.1195	8.143e-06	0.3918	0.3919	0.00024	80
14	Best: rs4902035 (2)	Gene	60.77-60.77Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7145344		60766603	0.09651	0.02153	0.001295	0.3468	0.00011	172
	rs4902035		60767005	0.09608	0.007151	0.0001006	0.5526	0.00036	64
15	Best: rs2414869 (2)	Gene	63.11-63.12Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2414869	MTFMT NCBI Gene Pubmed Genecard	63109919	0.1204	0.001197	0.01721	0.2542	0.00027	73
	rs2946653		63118820	0.1331	0.003681	0.003584	0.565	0.00013	148
16	Best: rs6499937 (2)	Gene	56.75-56.79Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6499937	CSNK2A2 NCBI Gene Pubmed Genecard	56753662	0.005612	1	1	1.295e-08	0.0028	20
	rs8056660	CSNK2A2 NCBI Gene Pubmed Genecard	56786849	0.008617	1	1	0.9117	0.00073	43
23	Best: SNP_A-1998393 (2)	Gene	24.36-24.44Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6526393	PCYT1B NCBI Gene Pubmed Genecard	24355404	0.01625	1	0.3149	0.7827	0.00015	119
	SNP_A-1998393		24435950	0.01139	0.0004369	0.05584	3.782e-07	0.00097	37
23	Best: rs5951179 (6)	Gene	70.69-70.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12012309		70686070	0.03134	0.1986	0.4686	0.02299	0.00011	187
	rs6625898		70861066	0.04722	1	0.2286	0.04832	0.00026	76
	rs6525524		70877954	0.04115	1	1	0.04641	0.00029	70
	rs6525525		70877990	0.04104	0.6796	1	0.06894	0.00032	65
	rs5951179	NHSL2 NCBI Gene Pubmed Genecard	70949622	0.04122	0.2565	0.7934	0.0002621	0.01	10
	rs7878231	NHSL2 NCBI Gene Pubmed Genecard	70961868	0.04442	1	0.7859	0.1585	0.0014	29
23	Best: rs5938070 (6)	Gene	74.34-74.47Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6607539	LOC646127 NCBI Gene Pubmed Genecard	74340701	0.02764	0.385	1	0.002872	0.00015	127
	rs2146767	ZDHHC15 NCBI Gene Pubmed Genecard	74420469	0.02662	1	0.6329	0.001825	0.00021	90
	rs4892579	ZDHHC15 NCBI Gene Pubmed Genecard	74428079	0.02725	0.372	0.6376	0.003325	0.00029	68
	rs4892583	ZDHHC15 NCBI Gene Pubmed Genecard	74448870	0.027	0.3596	1	0.003164	0.00012	157
	rs5938070	ZDHHC15 NCBI Gene Pubmed Genecard	74450099	0.02472	1	0.6378	8.33e-07	0.0078	13
	rs5981362	ZDHHC15 NCBI Gene Pubmed Genecard	74473479	0.02752	0.3725	1	0.002206	0.00017	105