T-Trees

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

Supplementary data

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1	Best: rs505444 (5)	Gene	52.95-53.03Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7518390	ZYG11B NCBI Gene Pubmed Genecard	52945395	0.4279	0.1273	0.5237	0.3701	0.00049	26
	rs10888755	ZYG11B NCBI Gene Pubmed Genecard	52952850	0.4159	0.8887	0.2256	0.4633	0.00025	60
	rs2065477	ZYG11B NCBI Gene Pubmed Genecard	52962234	0.4354	0.03316	0.1638	0.4766	0.00017	114
	rs505444	ZYG11B NCBI Gene Pubmed Genecard	52963881	0.4227	0.1161	0.0003718	0.05182	0.0006	21
	rs554301	ZYG11A NCBI Gene Pubmed Genecard	53033969	0.4091	0.1337	0.3057	0.6295	0.00015	142
1	Best: rs6683655 (4)	Gene	185.16-185.18Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs923408		185161903	0.4358	0.1281	0.192	0.8679	0.00028	49
	rs6683655		185168259	0.4357	0.1532	0.1793	0.7237	0.0011	16
	rs12137523		185173706	0.4442	0.1529	0.001468	0.3171	0.0006	22
	rs4396083		185179880	0.4357	0.1667	0.1921	0.8029	0.0006	23
2	Best: rs1453783 (2)	Gene	5.37-5.37Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10929488		5367555	0.3888	0.7726	0.2195	0.1825	0.00014	171
	rs1453783		5368662	0.3726	0.6616	0.01623	0.5627	0.00022	76
3	Best: rs326296 (8)	Gene	97.61-97.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9856790		97610163	0.2227	0.2203	0.9572	0.2639	0.00014	173
	rs9874467		97625924	0.429	0.02355	0.01821	0.5456	0.0022	9
	rs7614294		97626719	0.4863	0.0292	0.6073	0.6202	0.0014	13
	rs10934513		97626927	0.43	0.01258	0.05618	0.5319	0.0017	11
	rs11916855		97628365	0.487	0.2035	0.3395	0.5771	0.0018	10
	rs326296		97643917	0.446	1.035e-06	0.06675	2.05e-05	0.0067	4
	rs9829940		97650339	0.4196	0.5137	0.2283	0.8835	0.00017	115
	SNP_A-4302324		97665005	0.08169	0.5054	0.9079	0.01755	0.0053	5
3	Best: rs7434223 (4)	Gene	163.64-163.67Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11924705		163644318	0.4241	0.7763	3.435e-05	0.0003186	0.00053	25
	rs6789378		163650098	0.4164	0.5394	0.476	0.02372	0.00025	61
	rs9858104		163658445	0.4175	1	0.3887	0.0265	0.00019	101
	rs7434223		163666164	0.4155	0.6368	0.5734	0.02944	0.00055	24
4	Best: rs10014689 (2)	Gene	55.92-55.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10014689		55923198	0.02054	0.4984	0.6489	0.345	0.00015	154
	rs10003420		55930187	0.01993	1	0.265	5.573e-08	0.00013	192
4	Best: rs814376 (2)	Gene	117.36-117.39Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs814398		117357074	0.3855	0.6304	1	0.4842	0.00015	152
	rs814376		117390134	0.3921	0.5047	0.003559	0.7179	0.00021	81
6	Best: rs2621384 (6)	Gene	32.87-32.88Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2621384		32867251	0.3837	0.4114	0.9692	0.2986	0.0025	7
	rs2857161		32867275	0.3781	0.3818	0.969	0.3384	0.00024	67
	rs2157082		32868692	0.4393	0.5198	0.000395	0.2796	0.0012	14
	rs2857154		32870594	0.3839	0.6639	0.8461	0.7982	0.00049	27
	rs7382347		32883664	0.3825	0.5627	1	0.5106	0.00018	109
	rs2857129		32884601	0.3829	0.5623	0.9691	0.4968	0.00025	64
7	Best: rs2717992 (2)	Gene	37.11-37.12Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2724006	ELMO1 NCBI Gene Pubmed Genecard	37106976	0.4509	0.1693	0.004571	0.9668	0.00014	175
	rs2717992	ELMO1 NCBI Gene Pubmed Genecard	37115490	0.4461	0.1554	0.11	0.361	0.00022	77
7	Best: rs11575535 (3)	Gene	50.31-50.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11575537	DDC NCBI Gene Pubmed Genecard	50306094	0.01479	0.3822	1	0.549	0.00027	51
	rs11575535	DDC NCBI Gene Pubmed Genecard	50306203	0.01873	0.08135	1	0.1082	0.00042	33
	rs11575518	DDC NCBI Gene Pubmed Genecard	50309890	0.01762	1	1	0.005926	0.00025	63
8	Best: rs7460439 (2)	Gene	87.57-87.58Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4961196	FAM82B NCBI Gene Pubmed Genecard	87570826	0.49	0.3882	0.2125	0.9835	0.00014	167
	rs7460439	FAM82B NCBI Gene Pubmed Genecard	87583206	0.4481	0.8537	0.7651	0.1756	0.00023	73
9	Best: rs10121866 (2)	Gene	72.35-72.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10121866		72351403	0.4556	0.9273	1	0.192	0.00018	112
	rs7044241		72357097	0.4513	0.8911	0.1916	0.044	0.00013	193
9	Best: rs12343115 (2)	Gene	107.23-107.23Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12343115		107233702	0.005537	1	1	1.079e-10	0.00024	66
	rs10119737		107234139	0.009674	0.1758	0.23	0.7525	0.00019	92
10	Best: rs3122348 (12)	Gene	30.95-31.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1506784	LYZL2 NCBI Gene Pubmed Genecard	30949906	0.05529	0.0405	0.001374	0.6191	0.00016	137
	rs3122344		30969266	0.2517	0.5074	0.6973	0.981	0.0015	12
	rs16931816		30969354	0.03886	0.07171	0.6217	0.7488	0.00026	55
	rs16931818		30969434	0.0007114	1	1	0.445	0.00013	197
	SNP_A-2100739		30990735	0.07869	0.02921	0.7977	0.6736	0.029	2
	rs16931828	LOC645954 NCBI Gene Pubmed Genecard	30990752	0.1153	0.445	0.2366	0.5185	0.00042	34
	rs3122348	LOC645954 NCBI Gene Pubmed Genecard	30991151	0.03151	2.849e-05	1	5.572e-88	0.04	1
	rs7083541	LOC645954 NCBI Gene Pubmed Genecard	30997484	0.4881	0.8916	0.6332	0.3859	0.00046	28
	rs7078126	LOC645954 NCBI Gene Pubmed Genecard	31024312	0.07803	0.6296	1	0.7583	0.0022	8
	rs7093972	LOC645954 NCBI Gene Pubmed Genecard	31024349	0.07753	0.4234	0.523	0.9385	0.0012	15
	rs3858241	LOC645954 NCBI Gene Pubmed Genecard	31041299	0.06498	0.8515	0.02187	0.9333	0.0027	6
	rs1494134		31057878	0.145	0.925	0.4684	0.2297	0.00024	69
10	Best: rs1914139 (2)	Gene	113.20-113.22Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4423118		113195630	0.4409	0.3825	0.766	0.6777	0.00025	62
	rs1914139		113215843	0.4274	0.3507	0.123	0.1548	0.00045	29
10	Best: rs913525 (4)	Gene	125.23-125.25Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11248546		125232273	0.4579	0.8179	0.006736	0.01192	0.00035	40
	rs9423354		125239754	0.4545	0.9631	0.2809	0.1887	0.00019	94
	rs913525		125243227	0.4497	0.8541	0.5792	0.3194	0.00043	31
	rs2479901		125245063	0.451	0.8181	0.4373	0.254	0.00041	35
11	Best: rs7103691 (3)	Gene	11.10-11.11Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2403460		11103014	0.4901	0.4133	0.4161	0.2067	0.0004	36
	rs7103691		11107406	0.487	0.6493	0.3589	1	0.00061	20
	rs7110449		11107687	0.4714	0.7495	0.1407	0.7721	0.00014	174
11	Best: rs7126366 (2)	Gene	12.48-12.48Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4757537	PARVA NCBI Gene Pubmed Genecard	12478568	0.001425	1	1	0.01237	0.00017	118
	rs7126366	PARVA NCBI Gene Pubmed Genecard	12483472	0.004475	1	1	4.578e-07	0.00025	59
14	Best: rs17791722 (3)	Gene	103.34-103.36Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4900597	PPP1R13B NCBI Gene Pubmed Genecard	103336417	0.3319	0.4739	0.5904	0.8608	0.00013	184
	rs4906376	PPP1R13B NCBI Gene Pubmed Genecard	103341918	0.3244	0.5064	0.001442	0.1389	0.00017	117
	rs17791722	PPP1R13B NCBI Gene Pubmed Genecard	103355963	0.3321	0.5397	0.6188	0.7256	0.00023	71
22	Best: rs10212068 (8)	Gene	35.93-35.99Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs69264	SSTR3 NCBI Gene Pubmed Genecard	35928450	0.1968	0.5112	0.4553	0.4361	0.00014	178
	rs4821602	SSTR3 NCBI Gene Pubmed Genecard	35933689	0.4949	0.5247	0.7692	1	0.00019	99
	rs13053175		35937809	0.4493	0.4923	0.71	0.03587	0.00031	44
	rs1476002	RAC2 NCBI Gene Pubmed Genecard	35955288	0.1164	0.0009595	2.9e-05	0.5403	0.00015	145
	rs6000632		35968615	0.2581	0.9519	0.5672	0.4625	0.00017	116
	rs10212068		35969121	0.02827	1	0.002635	1.059e-57	0.02	3
	rs5750402		35985788	0.1709	0.3415	0.8959	0.5827	0.00039	37
	rs4820279		35991286	0.1741	0.238	0.7494	0.849	0.00027	50
22	Best: rs5764698 (3)	Gene	44.07-44.07Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5765273	SMC1B NCBI Gene Pubmed Genecard	44068489	0.466	0.8907	0.001427	0.01902	0.00022	80
	rs5764698	SMC1B NCBI Gene Pubmed Genecard	44070520	0.4584	0.8907	0.4174	0.2913	0.00042	32
	rs9614462	SMC1B NCBI Gene Pubmed Genecard	44071768	0.4609	1	0.3767	0.3206	0.00031	43
23	Best: rs2124012 (3)	Gene	2.70-2.96Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs311168	XG NCBI Gene Pubmed Genecard	2704201	0.3354	0.1299	0.6913	0.4651	0.0002	91
	rs211640	ARSE NCBI Gene Pubmed Genecard	2864372	0.487	0.6174	0.3282	0.8783	0.00017	125
	rs2124012	ARSF NCBI Gene Pubmed Genecard	2960417	0.3616	0.9124	0.1705	0.1578	0.00021	83
23	Best: rs5916413 (2)	Gene	3.81-3.81Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3859965		3808948	0.4539	0.05598	0.4682	0.4422	0.00018	106
	rs5916413		3810459	0.4704	0.1081	0.1803	0.4904	0.00027	52
23	Best: rs5916649 (2)	Gene	4.38-4.50Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5916649		4375551	0.4924	0.1328	0.3282	0.557	0.00013	187
	rs5915785		4497986	0.341	0.2346	0.06747	0.8297	0.00013	194
23	Best: rs4830882 (2)	Gene	13.43-13.43Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2361158		13428449	0.4553	0.2648	0.3513	0.7194	0.00013	188
	rs4830882	TCEANC NCBI Gene Pubmed Genecard	13433891	0.4729	0.1322	0.6433	0.7017	0.00014	172
23	Best: rs4240155 (3)	Gene	14.72-14.78Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5980078		14722059	0.4675	0.2305	0.8768	0.01636	0.00015	149
	rs5978704		14763020	0.4924	0.1082	0.8775	0.00365	0.00016	132
	rs4240155		14781196	0.4939	0.05739	0.8372	0.006892	0.00026	57
23	Best: rs1898744 (3)	Gene	26.83-26.90Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1898744		26825461	0.4826	0.07192	0.05102	0.9187	0.00034	41
	rs1898742		26863232	0.4477	0.0702	0.2542	0.6817	0.00015	150
	rs4829035		26904355	0.4729	0.4212	0.1223	0.7986	0.00024	68
23	Best: rs1948804 (4)	Gene	33.63-33.80Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17330535		33625060	0.4011	0.2161	0.01565	0.4978	0.00014	165
	rs11095312		33710762	0.4217	0.0677	0.0007632	0.6983	0.00023	74
	rs4829313		33787015	0.3902	0.3004	0.001483	0.5832	0.00016	127
	rs1948804		33798318	0.3877	0.2142	0.001801	0.9583	0.00027	53
23	Best: rs5928946 (3)	Gene	35.42-35.46Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5928946		35418194	0.4584	0.6158	0.01132	0.7012	0.00022	75
	rs7056322		35420739	0.4604	0.3096	0.04765	0.662	0.00021	82
	rs12842521		35460875	0.4602	0.5483	0.01734	0.6271	0.00014	166
23	Best: rs851234 (2)	Gene	45.93-45.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs851235		45927769	0.4422	0.3612	0.434	0.959	0.00015	147
	rs851234		45928270	0.4249	0.2618	0.1122	0.5194	0.0002	89
23	Best: rs4545257 (5)	Gene	87.94-89.23Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs847463		87943605	0.405	0.8351	0.02794	0.3633	0.00016	128
	rs7886656		88002136	0.4199	0.9158	0.04124	0.548	0.00014	179
	rs4545257		88003898	0.3972	0.08112	0.04812	0.3902	0.00019	93
	rs4893371		88196675	0.4204	0.6792	0.2661	0.07469	0.00017	121
	rs5941511		89228926	0.3536	0.5825	0.9553	0.8102	0.00013	196
23	Best: rs2498864 (6)	Gene	97.64-97.87Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5920671		97635686	0.4653	0.1936	0.1337	0.3439	0.00017	119
	rs1342223		97640103	0.4549	0.08868	0.2339	0.522	0.00013	190
	rs2335828		97740166	0.4549	0.2254	0.1078	0.2292	0.00016	129
	rs241863		97781312	0.4817	0.05523	0.08652	0.3437	0.00014	161
	rs241852		97800641	0.4819	0.2299	0.01789	0.5235	0.00014	163
	rs2498864		97870593	0.4543	0.05382	0.1084	0.8981	0.00019	98
23	Best: rs12557159 (2)	Gene	100.06-100.09Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12557159		100061887	0.4162	0.004298	0.2639	0.5012	0.0003	45
	rs7050888	TRMT2B NCBI Gene Pubmed Genecard	100088196	0.4761	0.2252	0.5028	0.1321	0.00016	130
23	Best: rs4829520 (2)	Gene	111.98-111.98Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4829520		111975806	0.4438	0.1809	0.5687	0.03763	0.0002	86
	rs5974328		111982209	0.4583	0.3606	0.5706	0.02779	0.00013	189
23	Best: rs6645482 (4)	Gene	115.40-115.74Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4824325	SLC6A14 NCBI Gene Pubmed Genecard	115396902	0.3861	0.09354	0.9146	0.01985	0.00018	107
	rs6646036		115664016	0.3833	0.02482	0.2112	0.7332	0.00022	79
	rs6645482		115696579	0.3639	0.006858	0.2002	0.8737	0.00023	72
	rs5910306		115742175	0.4432	0.1559	0.1919	0.7774	0.00015	148
23	Best: rs2278954 (3)	Gene	117.93-117.93Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2290514	LONRF3 NCBI Gene Pubmed Genecard	117929115	0.3614	0.003496	0.04557	0.3392	0.00014	169
	rs2278954	LONRF3 NCBI Gene Pubmed Genecard	117930111	0.3623	0.002582	0.03996	0.3676	0.00039	38
	rs2124399	LONRF3 NCBI Gene Pubmed Genecard	117931248	0.3597	0.001954	0.1976	0.3236	0.00015	155
23	Best: rs1858934 (2)	Gene	118.71-118.79Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2428982		118712230	0.498	0.002655	0.7191	0.939	0.00015	156
	rs1858934	NDUFA1 NCBI Gene Pubmed Genecard RNF113A NCBI Gene Pubmed Genecard	118786287	0.4977	0.005033	1	1	0.00016	138
23	Best: rs4824960 (2)	Gene	139.60-139.61Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4824960		139604982	0.4573	0.1027	1	0.1245	0.00017	120
	rs5907655		139610656	0.4489	0.06613	0.9175	0.2187	0.00014	180
23	Best: rs5965859 (6)	Gene	144.27-144.41Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs5965859		144274410	0.4405	0.004436	0.2504	0.1366	0.00032	42
	rs5919854		144279499	0.4401	0.001487	0.4315	0.1493	0.00018	102
	rs1151983		144324695	0.4733	0.006628	0.197	0.4285	0.00013	191
	rs754213		144328235	0.4741	0.003533	0.4084	0.4747	0.00023	70
	rs6525608		144341629	0.4717	0.01229	0.215	0.1761	0.00029	48
	rs5920606		144412260	0.4729	0.1612	0.6424	0.2507	0.00019	95
23	Best: rs6525652 (2)	Gene	145.03-145.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6525652		145032433	0.4229	0.1549	0.1417	0.4092	0.00015	144
	rs4827702		145055899	0.4188	0.4132	0.1033	0.4852	0.00014	181