T-Trees

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

Supplementary data

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1	Best: rs825148 (6)	Gene	219.90-219.97Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1914612	SUSD4 NCBI Gene Pubmed Genecard	219900169	0.03478	0.4904	1	0.7784	0.00093	78
	SNP_A-4236822		219903154	0.03413	0.2739	0.04881	0.7761	0.00086	85
	rs12074782		219946890	0.04217	1	0.6574	0.6074	0.002	42
	rs2678370		219965833	0.04058	0.3657	0.2381	0.7139	0.0023	37
	rs2678369		219965851	0.04082	0.7674	0.2388	0.7543	0.0024	36
	rs825148		219967019	0.05298	2.41e-210	0.01382	5.213e-13	0.045	3
2	Best: rs1870340 (3)	Gene	96.53-96.54Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12052336		96528325	0.01865	1	1	0.7032	0.0013	62
	rs1870340		96538827	0.02738	3.159e-122	0.6301	4.889e-08	0.016	9
	rs12614696		96540831	0.01957	1	0.6325	0.5511	0.0014	57
2	Best: rs935019 (2)	Gene	127.16-127.17Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs935019	GYPC NCBI Gene Pubmed Genecard	127162719	0.2605	5.856e-13	0.8874	0.009614	0.001	74
	rs10174588		127171100	0.3401	0.298	0.8027	0.02925	0.00014	159
4	Best: rs16837871 (11)	Gene	6.06-6.08Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7679272		6057618	0.2297	0.3671	0.7932	0.9803	0.0018	45
	rs16837871		6059184	0.1478	8.617e-23	0.2844	1.753e-28	0.016	10
	rs7664218		6060685	0.1851	0.7649	0.462	0.9153	0.0067	20
	rs7664229		6060707	0.1849	0.8227	0.5801	0.8107	0.0061	22
	rs7691494		6060721	0.1852	0.823	0.5398	0.8317	0.007	19
	rs6446412	C4orf50 NCBI Gene Pubmed Genecard	6079898	0.3688	0.1471	0.72	0.3041	0.00017	148
	rs7695500	C4orf50 NCBI Gene Pubmed Genecard	6079959	0.3665	0.1594	0.6041	0.4275	0.00011	171
	rs13107008	C4orf50 NCBI Gene Pubmed Genecard	6080067	0.375	0.1508	0.9055	0.2324	0.00018	144
	rs7434820	C4orf50 NCBI Gene Pubmed Genecard	6081537	0.3339	0.03929	0.2581	0.1252	0.00013	161
	rs4519747	C4orf50 NCBI Gene Pubmed Genecard	6081848	0.34	0.06561	0.2284	0.07733	0.00013	162
	rs6826497	C4orf50 NCBI Gene Pubmed Genecard	6083331	0.3393	0.04642	0.3184	0.08093	0.00011	178
4	Best: rs1553460 (11)	Gene	17.85-17.92Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1039539		17850862	0.258	0.5536	0.3804	0.7214	0.00061	98
	rs17523800		17870443	0.3665	0.09689	0.9367	0.8638	0.0012	64
	rs11938418		17871212	0.2839	0.9115	0.03268	0.9088	0.0017	50
	rs1553460		17872130	0.3102	1.415e-94	2.877e-05	2.415e-24	0.025	6
	rs1503881		17878898	0.2723	0.195	0.3237	0.2757	0.00044	109
	rs1503882		17878953	0.2718	0.1762	0.3966	0.2364	0.00044	111
	rs4698673		17885266	0.276	0.1446	0.5442	0.3793	0.00022	137
	rs6857578		17896563	0.2783	0.2021	0.5459	0.1813	0.00013	167
	rs6835889		17896783	0.2605	0.2719	0.9613	0.2038	0.00013	165
	rs2080231		17912133	0.2644	0.167	0.5284	0.04958	0.0001	180
	rs16896754		17919801	0.114	0.7438	0.6414	0.3801	8.9e-05	190
4	Best: rs6840033 (5)	Gene	141.58-141.62Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs868653	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141577389	0.08771	0.164	0.09089	0.3549	0.0014	60
	rs6840033	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141586466	0.2063	4.642e-19	0.9156	2.345e-11	0.0031	30
	rs6825404	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141605361	0.1182	0.08176	0.8598	0.9236	9.5e-05	185
	rs12509386	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141611515	0.1118	0.2054	1	0.7932	9.5e-05	186
	rs16998462	LOC100129858 NCBI Gene Pubmed Genecard SCOC NCBI Gene Pubmed Genecard	141622476	0.1122	0.1344	1	0.7683	8.6e-05	194
6	Best: rs10499044 (2)	Gene	107.25-107.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10499044		107247988	0.1045	2.371e-18	0.001966	6.596e-13	0.0028	34
	rs2798360		107255166	0.1461	0.1762	0.9404	0.6596	0.00032	119
7	Best: rs1528356 (16)	Gene	120.71-120.72Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1919096		120707046	0.05549	1	1	0.4704	0.0017	53
	rs1919095		120707076	0.05482	0.654	0.861	0.525	0.002	40
	rs2896304		120708523	0.05576	1	0.8638	0.417	0.0018	46
	rs4727930		120708949	0.05516	1	1	0.4417	0.0017	49
	rs1919090		120712018	0.05545	1	0.8618	0.5883	0.0017	52
	rs10229163		120712149	0.05462	0.1677	0.5996	0.3877	0.0016	55
	rs10261636		120712512	0.04951	0.3176	0.03192	0.5022	0.0016	56
	rs7791809		120713013	0.05701	0.8303	1	1	0.00092	79
	rs4451245		120715189	0.05543	1	1	0.4704	0.0019	44
	rs1528358		120715223	0.05627	0.654	0.6151	0.2433	0.0022	38
	rs1528356		120715406	0.06613	7.097e-264	0.004003	3.198e-22	0.059	1
	rs1534528		120715973	0.05716	1	0.7434	0.1071	0.0017	51
	rs7793149		120716897	0.05523	1	1	0.4427	0.002	43
	rs4731018		120717374	0.05517	1	0.8612	0.5874	0.0016	54
	rs4731020		120717469	0.05125	0.02079	0.002834	0.2595	0.002	39
	rs10235141		120720024	0.05504	1	1	0.4147	0.0018	47
8	Best: rs7837736 (2)	Gene	15.34-15.35Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7837736		15341074	0.1218	2.916e-75	0.1452	1.345e-102	0.059	2
	rs1908465		15352804	0.2839	0.03695	0.5201	0.1759	0.0038	27
9	Best: rs17797701 (4)	Gene	1.79-1.81Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17724676		1789272	0.02169	1	0.07245	0.1786	0.0013	63
	rs4142985		1809662	0.0217	1	0.6695	0.2287	0.0012	66
	rs1556412		1813898	0.02153	1	0.4036	0.3547	0.0014	58
	rs17797701		1814888	0.01434	1.99e-09	0.4026	1.43e-20	0.0093	13
10	Best: rs2393191 (2)	Gene	58.39-58.41Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2393191		58394623	0.01577	0.3108	0.5761	0.2455	0.00075	92
	rs16909905		58410545	0.01209	1	0.3568	0.9247	0.00062	97
11	Best: rs17116117 (21)	Gene	113.02-113.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17610557		113018709	0.1318	0.8405	0.3389	0.502	0.00038	113
	rs17532157		113021980	0.1308	0.8405	0.1074	0.668	0.00033	116
	rs17532479		113028191	0.132	1	0.4256	0.5418	0.00028	122
	rs11606746		113042520	0.1295	0.9178	0.8071	0.4951	0.00025	126
	rs17611093		113053519	0.1297	0.2578	0.1696	0.4785	0.00027	124
	rs11604887		113108019	0.1254	0.7518	0.868	0.5125	0.00033	117
	rs17541153	ZW10 NCBI Gene Pubmed Genecard	113120832	0.1238	0.7513	0.2357	0.7064	0.00032	118
	rs1633550	USP28 NCBI Gene Pubmed Genecard	113174415	0.127	0.7548	0.8693	0.5348	0.00061	99
	rs1633548	USP28 NCBI Gene Pubmed Genecard	113176716	0.1266	1	0.5062	0.7794	0.00053	105
	rs1713671	USP28 NCBI Gene Pubmed Genecard	113180048	0.4215	0.7107	0.1031	0.503	0.00012	170
	rs2513574	USP28 NCBI Gene Pubmed Genecard	113186515	0.1265	0.8338	0.804	0.4925	0.00054	104
	rs2519200	USP28 NCBI Gene Pubmed Genecard	113190019	0.2445	0.8068	0.8808	0.9425	0.0004	112
	rs4936283	USP28 NCBI Gene Pubmed Genecard	113218600	0.4644	0.2362	0.3933	0.9669	8.6e-05	193
	rs10789970	HTR3B NCBI Gene Pubmed Genecard	113279156	0.4083	0.4541	0.9695	0.6438	0.00018	143
	rs7396105	HTR3B NCBI Gene Pubmed Genecard	113291749	0.4065	0.708	0.9084	0.5698	0.00023	132
	rs17116117	HTR3B NCBI Gene Pubmed Genecard	113306801	0.05276	9.736e-06	0.116	1.158e-31	0.013	12
	rs17116145	HTR3B NCBI Gene Pubmed Genecard	113309536	0.02946	0.4044	0.5202	0.7136	0.00065	94
	rs1176741	HTR3B NCBI Gene Pubmed Genecard	113312525	0.03132	0.2589	0.1192	0.8128	0.00082	87
	rs1176740	HTR3B NCBI Gene Pubmed Genecard	113312606	0.03151	1	0.1206	0.8593	0.00089	80
	rs1176739	HTR3B NCBI Gene Pubmed Genecard	113313027	0.03193	1	0.3693	0.9065	0.00088	82
	rs1176738	HTR3B NCBI Gene Pubmed Genecard	113313305	0.03135	0.2589	0.1193	0.8128	0.00087	83
12	Best: rs10843660 (11)	Gene	30.25-30.28Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10743704		30249349	0.2972	0.4792	0.402	0.7688	0.0065	21
	rs10771657		30250561	0.4332	0.3825	0.4742	0.3589	0.00058	101
	rs10843660		30259724	0.3795	2.737e-65	0.03536	9.177e-35	0.031	5
	rs9669515		30260529	0.2957	0.5128	0.4791	0.7514	0.0075	17
	rs11050722		30262092	0.1215	0.6557	0.3999	0.1284	0.00012	169
	rs1157480		30264271	0.2963	0.4119	0.3771	0.5558	0.0074	18
	rs1385567		30267520	0.1222	0.7399	0.07765	0.1546	0.00016	150
	rs4931292		30271808	0.3172	0.2923	0.9312	0.233	0.00078	89
	rs7970841		30274289	0.3077	0.2245	0.8962	0.5607	0.00056	103
	rs10843669		30276019	0.3085	0.37	0.9308	0.546	0.00057	102
	rs977924		30282488	0.3098	0.3699	0.8286	0.6711	0.0005	107
13	Best: rs17667894 (4)	Gene	90.79-90.83Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11842349		90793937	0.0328	0.4241	0.3918	0.3241	0.004	25
	rs17667894		90812310	0.02048	1	0.3776	2.821e-42	0.022	7
	rs17667973		90823894	0.03875	0.5167	0.01391	0.4218	0.0011	70
	rs17735544		90825251	0.03366	0.4349	0.09197	0.3028	0.0036	28
15	Best: rs2865199 (2)	Gene	77.69-77.69Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16971150		77685718	0.01841	0.4576	0.6257	0.7012	0.00097	76
	rs2865199		77690427	0.01273	1	0.6257	2.347e-13	0.0032	29
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	0.005564	1	1	2.2e-08	0.0012	68
	rs8056660	CSNK2A2 NCBI Gene Pubmed Genecard	56786849	0.008598	1	1	1	0.00015	151
16	Best: rs16955238 (5)	Gene	79.96-79.98Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs8057691	GAN NCBI Gene Pubmed Genecard	79958244	0.03318	0.2592	1	0.2044	0.00013	166
	SNP_A-2162323		79970090	0.02089	1	0.4036	0.1484	0.0012	67
	rs16955238		79973192	0.02742	4.818e-114	0.6464	2.449e-05	0.015	11
	rs16955255	LOC100996430 NCBI Gene Pubmed Genecard	79977632	0.02078	1	0.4026	0.1933	0.001	72
	rs16955259	LOC100996430 NCBI Gene Pubmed Genecard	79977690	0.02108	1	0.4036	0.1959	0.001	73
17	Best: SNP_A-1948953 (2)	Gene	17.27-17.27Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16961675	SMCR9 NCBI Gene Pubmed Genecard	17266676	0.3221	0.5993	0.3353	0.1707	8.4e-05	199
	SNP_A-1948953		17267088	0.2792	2.842e-26	0.005177	2.1e-06	0.0055	23
22	Best: rs8137391 (6)	Gene	27.70-27.75Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16986925	ZNRF3 NCBI Gene Pubmed Genecard	27703441	0.01259	1	0.3887	0.7122	0.00064	96
	rs4823000	ZNRF3 NCBI Gene Pubmed Genecard	27704445	0.01627	0.3694	0.5684	0.6245	8.8e-05	192
	rs11912198	ZNRF3 NCBI Gene Pubmed Genecard	27711924	0.01264	1	0.3975	0.6433	0.0003	121
	rs5752850	ZNRF3 NCBI Gene Pubmed Genecard	27722931	0.013	1	0.4205	0.5245	0.0005	106
	rs16986990	ZNRF3 NCBI Gene Pubmed Genecard ZNRF3-AS1 NCBI Gene Pubmed Genecard	27745369	0.01535	1	1	0.5568	0.0011	71
	rs8137391	ZNRF3 NCBI Gene Pubmed Genecard ZNRF3-AS1 NCBI Gene Pubmed Genecard	27746781	0.009938	1	1	1.487e-19	0.0087	16
23	Best: rs5951179 (2)	Gene	70.95-70.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5951179	NHSL2 NCBI Gene Pubmed Genecard	70949622	0.04045	0.2548	1	0.0003442	0.0039	26
	rs7878231	NHSL2 NCBI Gene Pubmed Genecard	70961868	0.0437	1	1	0.189	0.00025	128