T-Trees

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

Supplementary data

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1	Best: rs12409315 (2)	Gene	3.25-3.26Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs12409315	PRDM16 NCBI Gene Pubmed Genecard	3252415	0.07704	0.1751	0.004369	0.002537	0.00044	32
	rs6687835	PRDM16 NCBI Gene Pubmed Genecard	3260331	0.3205	0.165	0.9328	0.4091	0.00026	52
1	Best: rs11209026 (10)	Gene	67.31-67.46Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs7515029		67308393	0.03591	0.5289	0.19	5.012e-10	0.00036	38
	rs4655679		67311678	0.2728	0.2111	0.2108	6.104e-08	7.5e-05	168
	rs11805303	IL23R NCBI Gene Pubmed Genecard	67387537	0.3442	0.545	0.1357	1.239e-12	0.00017	83
	rs2863212	IL23R NCBI Gene Pubmed Genecard	67397137	0.1043	0.8964	0.3265	0.7528	0.00032	47
	rs10489629	IL23R NCBI Gene Pubmed Genecard	67400370	0.4296	0.5063	0.3479	8.652e-12	0.00026	50
	SNP_A-2045577		67401629	0.3029	0.2185	0.5557	1.362e-09	0.00019	72
	rs2201841	IL23R NCBI Gene Pubmed Genecard	67406223	0.3445	0.419	0.2885	1.405e-11	0.00079	20
	rs10489628	IL23R NCBI Gene Pubmed Genecard	67416128	0.3751	0.6369	0.7852	0.001663	0.00015	91
	rs11209026	IL23R NCBI Gene Pubmed Genecard	67417979	0.0451	1	3.524e-05	8.238e-18	0.0052	5
	rs12119179		67459436	0.3502	0.3142	0.3547	1.546e-10	0.00013	104
1	Best: rs11162341 (2)	Gene	77.61-77.62Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11162341	AK5 NCBI Gene Pubmed Genecard	77609734	0.1323	0.4009	0.3784	0.8994	0.00023	57
	rs6658302	AK5 NCBI Gene Pubmed Genecard	77621006	0.2553	1	1.413e-05	0.1681	9.8e-05	140
1	Best: rs6677092 (5)	Gene	236.50-236.50Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2065914	RPS7P5 NCBI Gene Pubmed Genecard	236496837	0.4357	0.1892	0.05036	0.3105	6.4e-05	196
	rs12130657	RPS7P5 NCBI Gene Pubmed Genecard	236498157	0.4365	0.2056	0.05946	0.4113	0.0001	134
	rs6429174	RPS7P5 NCBI Gene Pubmed Genecard	236498436	0.3466	0.707	0.8082	0.1628	0.00033	45
	rs6677092	RPS7P5 NCBI Gene Pubmed Genecard	236499323	0.3726	3.01e-06	1	0.0001771	0.00042	33
	rs10926061	RPS7P5 NCBI Gene Pubmed Genecard	236499743	0.4357	0.1087	0.05991	0.3314	0.00018	76
2	Best: rs11887827 (35)	Gene	81.58-81.85Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11887827		81577812	0.3109	1.536e-07	1	2.423e-08	0.01	1
	rs17020244		81579712	0.1488	0.1567	1	0.976	0.0057	4
	rs12623313		81581046	0.1486	0.2162	1	1	0.0043	6
	rs10520335		81581185	0.1485	0.1559	0.9416	0.9041	0.0035	8
	rs7593114		81585945	0.326	0.9116	0.9668	0.1436	0.0094	2
	rs9646997		81586635	0.1489	0.08993	0.8838	0.8333	0.0014	14
	rs11126813		81587078	0.1487	0.1546	1	0.976	0.00073	22
	rs7570013		81593778	0.1752	0.5556	0.5264	0.5544	0.00013	97
	rs17020301		81594169	0.08116	0.6397	0.6139	0.3885	0.0028	10
	rs12613517	LOC100507201 NCBI Gene Pubmed Genecard	81599721	0.1488	0.1855	1	0.9043	0.0021	12
	rs11689930	LOC100507201 NCBI Gene Pubmed Genecard	81600746	0.1489	0.2564	1	0.9521	0.00022	59
	rs1052397	LOC100507201 NCBI Gene Pubmed Genecard	81601323	0.07482	0.2278	0.07635	0.7125	0.00021	63
	rs7575690	LOC100507201 NCBI Gene Pubmed Genecard	81601874	0.1492	0.1878	1	0.9044	0.00011	121
	rs17020333	LOC100507201 NCBI Gene Pubmed Genecard	81602132	0.1494	0.1864	0.942	0.9761	0.00015	89
	rs12468325	LOC100507201 NCBI Gene Pubmed Genecard	81602238	0.3259	0.8247	1	0.1778	0.00026	51
	rs17020366		81636536	0.08192	0.0667	1	0.2574	0.00064	26
	rs6752979		81653408	0.3163	0.8217	0.8324	0.1602	0.00011	122
	rs17608009		81669310	0.1748	0.7953	0.8511	0.1083	0.00041	34
	rs6725541		81671346	0.2426	0.5888	0.2783	0.04063	0.00034	44
	rs17020436		81681220	0.08215	1	0.3231	0.7255	0.00018	79
	rs6715049		81684652	0.3261	1	0.9337	0.1002	9.3e-05	147
	rs934894		81685585	0.1826	0.5042	0.8088	0.1023	0.00022	60
	rs7578937		81712443	0.2417	0.4155	0.299	0.04018	0.0001	130
	rs17608758		81716617	0.1759	0.6679	0.8516	0.129	7.1e-05	179
	rs12464902		81724164	0.06435	0.2044	0.4574	0.2758	0.0013	16
	rs7607015		81724939	0.06761	0.3123	0.2548	0.3055	0.0006	27
	rs1371109		81727952	0.3177	1	0.833	0.1236	0.00079	21
	rs17020502		81739719	0.3146	0.8655	0.7662	0.2049	0.00035	40
	rs10520329		81750166	0.1306	0.5299	0.9348	0.7994	7.1e-05	180
	rs17020570		81758512	0.1311	0.4631	0.7448	0.8491	0.00012	114
	rs11673915		81788508	0.1802	0.5511	0.6263	0.04206	0.0002	65
	rs1344969		81842139	0.1815	0.7346	0.9517	0.04256	0.00018	80
	rs11673909		81844485	0.2381	0.9454	0.1218	0.03935	9.8e-05	137
	rs11691608		81844974	0.2369	0.945	0.1477	0.02351	0.00013	102
	rs12612468		81847650	0.08437	1	0.9024	0.2984	0.00018	77
2	Best: SNP_A-2293058 (2)	Gene	143.22-143.28Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs13025041		143215865	0.07948	0.0536	0.2202	0.1651	8e-05	158
	SNP_A-2293058		143281926	0.002588	1	1	1.786e-05	0.00018	78
2	Best: rs10210302 (5)	Gene	233.94-233.97Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10210302	ATG16L1 NCBI Gene Pubmed Genecard	233940839	0.4515	0.425	0.01984	2.216e-13	0.00031	48
	rs6752107	ATG16L1 NCBI Gene Pubmed Genecard	233943448	0.4516	0.3973	0.02188	3.605e-13	0.00016	87
	rs6431654	ATG16L1 NCBI Gene Pubmed Genecard	233943769	0.4508	0.4848	0.02906	2.548e-13	0.0002	67
	rs3828309	ATG16L1 NCBI Gene Pubmed Genecard	233962410	0.452	0.5175	0.02892	1.185e-12	0.00013	99
	rs3792106	ATG16L1 NCBI Gene Pubmed Genecard	233972740	0.3968	0.1417	0.02814	3.323e-11	0.00012	108
3	Best: rs17047422 (2)	Gene	7.49-7.50Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9877337	GRM7 NCBI Gene Pubmed Genecard	7493853	0.001605	1	1	0.005798	7.8e-05	161
	rs17047422	GRM7 NCBI Gene Pubmed Genecard	7497152	0.001183	1	1	0.0003451	0.00019	73
3	Best: rs6774 (2)	Gene	120.41-120.42Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6774	B4GALT4 NCBI Gene Pubmed Genecard	120413574	0.1077	0.2495	0.0007103	0.01393	0.00034	43
	rs6766503	B4GALT4 NCBI Gene Pubmed Genecard	120423073	0.07651	0.003238	0.2234	0.2594	0.0002	70
3	Best: rs4686733 (2)	Gene	187.31-187.35Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs4686733		187313216	0.05322	6.501e-05	0.01116	0.3651	0.00014	93
	rs9835936	DGKG NCBI Gene Pubmed Genecard	187348945	0.4914	0.8478	0.9706	0.4668	6.3e-05	199
4	Best: rs1872321 (2)	Gene	86.13-86.18Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1872321	WDFY3 NCBI Gene Pubmed Genecard	86127973	0.002043	1	1	6.876e-09	0.0012	17
	rs12501332	WDFY3 NCBI Gene Pubmed Genecard	86184371	0.4259	0.9607	0.01599	0.2256	6.4e-05	198
4	Best: rs17045935 (2)	Gene	114.61-114.62Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17045935	ANK2 NCBI Gene Pubmed Genecard	114612173	0.09479	0.2384	0.0001068	0.05276	0.00026	53
	rs2272229	ANK2 NCBI Gene Pubmed Genecard	114618245	0.0964	0.1528	0.002778	0.09526	0.00012	107
4	Best: rs1595154 (3)	Gene	178.27-178.28Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1595154		178272461	0.002476	1	1	1.082e-07	0.00057	28
	rs7694356		178277407	0.00353	1	1	0.3679	7.5e-05	165
	rs13434489		178283098	0.005244	1	1	0.2999	0.00017	84
5	Best: rs17234657 (10)	Gene	40.43-40.53Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10512734		40429362	0.2853	0.4381	0.6972	6.014e-11	6.8e-05	187
	rs16869934		40433109	0.267	0.3042	0.7541	1.002e-11	9.9e-05	135
	rs17234657		40437266	0.1455	0.4176	0.3509	1.723e-13	0.00046	30
	rs6883686		40438290	0.4127	0.6914	0.6214	0.5145	6.5e-05	195
	rs6885315		40465299	0.4188	0.7662	0.622	0.5004	6.4e-05	197
	rs9292777		40473705	0.3663	0.1364	0.3147	5.787e-13	0.0002	69
	rs10213846		40478626	0.2989	0.4488	0.5558	8.037e-13	0.00026	54
	rs11957215		40481438	0.2994	0.5286	0.5283	5.777e-13	6.5e-05	193
	rs6871834		40515944	0.2962	0.2281	0.6724	1.963e-12	8.6e-05	153
	rs1505992		40534334	0.2911	0.4481	0.01437	1.201e-09	0.00013	101
6	Best: rs16884693 (2)	Gene	21.33-21.35Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16884693	CDKAL1 NCBI Gene Pubmed Genecard	21330730	0.003642	1	1	0.001212	9.4e-05	145
	rs6925942		21353408	0.07287	0.4066	0.01501	0.1173	8.9e-05	151
6	Best: rs2784899 (3)	Gene	129.84-129.84Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2784893	LAMA2 NCBI Gene Pubmed Genecard	129841194	0.2801	0.3157	0.4084	0.6001	0.0001	129
	rs2784899	LAMA2 NCBI Gene Pubmed Genecard	129844705	0.2603	0.8058	0.5247	0.06477	0.00013	106
	rs2784900	LAMA2 NCBI Gene Pubmed Genecard	129844815	0.2553	0.2135	0.5234	0.3378	0.00011	127
7	Best: rs10270692 (2)	Gene	35.37-35.37Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10270692		35367203	0.06599	1	0.6675	0.09305	0.0002	68
	rs12540338		35369481	0.1385	0.0009305	0.112	0.1622	0.00018	82
7	Best: rs6947579 (9)	Gene	125.13-125.16Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6942778		125126237	0.4107	0.7279	0.9696	0.5001	0.00012	116
	rs2158214		125126607	0.3378	0.1474	0.3421	0.9819	0.00025	55
	rs2107062		125126698	0.2992	9.335e-10	0.2447	5.603e-05	0.0038	7
	rs6947579		125126957	0.3172	0.2446	0.7017	0.8541	0.0075	3
	rs6967968		125127253	0.3173	0.2439	0.6706	0.8361	0.0014	15
	rs1419584		125137814	0.3174	0.2023	0.6395	0.8721	0.002	13
	rs1419585		125138283	0.3183	0.2229	0.5241	0.7828	0.00034	42
	rs1345220		125139094	0.3173	0.2911	0.7011	0.8538	0.00069	23
	rs1419555		125163392	0.3846	0.7248	0.6102	0.2808	0.00015	90
8	Best: rs10216909 (2)	Gene	129.90-129.92Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs16903632		129895741	0.003318	1	1	0.0002341	7.9e-05	160
	rs10216909		129924647	0.003212	1	1	7.763e-05	0.0001	131
10	Best: rs11011417 (2)	Gene	38.31-38.38Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11011417		38311123	0.001181	1	1	1.852e-05	0.00013	100
	rs581482	ZNF33A NCBI Gene Pubmed Genecard	38379327	0.06805	0.09411	0.03715	0.671	6.8e-05	186
11	Best: rs9804490 (2)	Gene	14.16-14.16Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs9804490		14160768	0.4586	1.495e-10	1.442e-06	2.407e-05	0.00012	117
	rs10766163		14161064	0.4335	0.6626	0.7625	0.02334	7.1e-05	178
12	Best: rs11613902 (2)	Gene	42.78-42.80Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs11613902	TMEM117 NCBI Gene Pubmed Genecard	42783505	0.09888	3.983e-07	0.09761	0.9427	0.00035	41
	rs12315961	TMEM117 NCBI Gene Pubmed Genecard	42796636	0.1025	0.3809	0.09772	0.2036	0.00021	64
14	Best: rs10144260 (4)	Gene	84.39-84.43Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs1601029		84385395	0.4993	0.9235	0.6053	0.1576	6.5e-05	194
	rs856663		84413383	0.0003211	1	1	0.05149	9.6e-05	142
	rs10144260		84425325	0.007638	1	1	1.177e-09	0.0011	18
	rs856696		84434683	0.4739	1	0.7366	0.2702	8.3e-05	154
14	Best: rs2819467 (2)	Gene	104.47-104.53Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs10083490		104473463	0.4574	0.8845	0.7381	0.452	7.4e-05	172
	rs2819467	C14orf79 NCBI Gene Pubmed Genecard	104530554	0.01051	0.3214	1	0.001513	0.00012	110
16	Best: rs2076756 (3)	Gene	49.30-49.31Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs17221417	NOD2 NCBI Gene Pubmed Genecard	49297083	0.3128	0.01604	0.2237	6.878e-12	8.2e-05	156
	rs2066843	NOD2 NCBI Gene Pubmed Genecard	49302700	0.2851	0.001923	0.3608	5.959e-13	0.00022	61
	rs2076756	NOD2 NCBI Gene Pubmed Genecard	49314382	0.2699	0.004495	0.7621	3.952e-15	0.00064	25
23	Best: rs5904497 (8)	Gene	21.69-21.74Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6629434		21690982	0.4454	0.5332	0.7919	0.5107	0.00017	85
	rs5951658		21699232	0.4446	0.5764	0.9164	0.5598	9.5e-05	143
	rs6629443	SMS NCBI Gene Pubmed Genecard	21729725	0.2339	0.6674	0.2058	0.6077	0.00067	24
	rs4824171	SMS NCBI Gene Pubmed Genecard	21732111	0.2837	0.6517	0.2142	0.3477	0.0026	11
	rs5904497	SMS NCBI Gene Pubmed Genecard	21732484	0.2728	5.965e-06	0.1496	0.04406	0.0033	9
	rs2238962	SMS NCBI Gene Pubmed Genecard	21733540	0.2436	0.6834	0.5783	0.2979	0.0001	133
	rs2040357	SMS NCBI Gene Pubmed Genecard	21738484	0.3066	0.6708	0.5044	0.1495	9.6e-05	141
	rs2283723	SMS NCBI Gene Pubmed Genecard	21740152	0.3239	0.7308	0.1118	0.08383	9.5e-05	144
23	Best: rs6624585 (2)	Gene	70.94-70.94Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6624585	NHSL2 NCBI Gene Pubmed Genecard	70943258	0.06773	0.7756	1	0.02692	0.00022	58
	rs11798652	NHSL2 NCBI Gene Pubmed Genecard	70943877	0.06498	0.3666	1	0.00069	0.0002	66