Table 1. Top PrediXcan results for WTCCC using DGN whole blood prediction models.

PrediXcan results for bonferroni significant gene associations. To account for multiple testing, we used a significance threshold of 5.76×10⁻⁶ for all diseases. Chromosome and gene start position are based on GENCODE version 12. The cross validated prediction R² between predicted and observed gene expression is based on 10-fold cross validation within the DGN whole blood sample.

Disease	Gene	Evidence	Chr	TSS	PrediXc an Z- Statistic	PrediXc an P- value	No. of SNPs in Predictor	Cross Validated Prediction R2
RA	DCLRE1B	V	1	114,447, 763	−6.68	2.46E-11	4	0.0388
RA	PTPN22	G	1	114,356, 433	5.67	1.44E-08	32	0.0795
BD	PTPRE		10	129,705, 325	4.94	7.71E-07	38	0.0355
CD	ATG16L1	G	2	234,118, 697	6.37	1.94E-10	20	0.0638
CD	IL23R	G	1	67,632,0 83	5.23	1.74E-07	38	0.0378
CD	APEH	V	3	49,711,4 35	5.14	2.77E-07	31	0.1164
CD	ZNF300	G ‡	5	150,273, 954	−4.98	6.29E-07	34	0.0387
CD	NKD1	G	16	50,582,2 41	−4.91	8.91E-07	43	0.0693
CD	BSN	G ‡	3	49,591,9 22	−4.68	2.89E-06	39	0.2336
CD	GPX1	V	3	49,394,6 09	−4.62	3.87E-06	28	0.0211
CD	SLC22A5	G ‡	5	131,705, 444	−4.54	5.75E-06	42	0.6356
HT	KCNN4		19	44,270,6 85	−4.7	2.62E-06	81	0.4655
T1D	DCLRE1B	V	1	114,447, 763	−7.84	4.34E-15	4	0.0388
T1D	ZNF165	M	6	28,048,7 53	7.3	2.92E-13	19	0.0374
T1D	ERBB3	G	12	56,473,6 41	−6.81	1.01E-11	9	0.2206
T1D	EGFL8	H	6	32,132,3 60	6.33	2.52E-10	36	0.0558
T1D	C6orf136	H	6	30,614,8 16	−6.33	2.52E-10	15	0.0137
T1D	HCG27	H	6	31,165,5 37	−6.33	2.52E-10	81	0.3721
T1D	GTF2H4	H	6	30,875,9 61	6.33	2.52E-10	69	0.0982
T1D	DDR1	H	6	30,844,1 98	6.33	2.52E-10	48	0.1427
T1D	AGER	H	6	32,148,7 45	−6.33	2.52E-10	39	0.0502
T1D	POU5F1	H	6	31,130,2 53	6.33	2.52E-10	45	0.2874
T1D	ATP6V1G2	H	6	31,512,2 39	6.33	2.52E-10	95	0.2543
T1D	TUBB	H	6	30,687,9 78	6.33	2.52E-10	56	0.0295
T1D	AIF1	H	6	31,582,9 61	6.33	2.52E-10	34	0.039
T1D	CYP21A2	H	6	32,006,0 42	−6.33	2.52E-10	80	0.229
T1D	LSM2	H	6	31,765,1 73	6.33	2.52E-10	31	0.0317
T1D	VARS2	H	6	30,876,0 19	6.33	2.52E-10	87	0.3628
T1D	APOM	H	6	31,620,1 93	−6.33	2.52E-10	58	0.0699
T1D	DDAH2	H	6	31,694,8 15	−6.33	2.52E-10	32	0.1943
T1D	NCR3	H	6	31,556,6 72	−6.33	2.52E-10	79	0.2548
T1D	ZSCAN16	M	6	28,092,3 38	6.16	7.37E-10	34	0.0291
T1D	ZKSCAN4	M	6	28,212,4 01	6.15	7.73E-10	17	0.0991
T1D	PTPN22	G	1	114,356, 433	5.83	5.41E-09	32	0.0795
T1D	RPS26	G ‡	12	56,435,6 37	5.82	6.00E-09	23	0.0719
T1D	GDF11	V	12	56,137,0 64	−5.75	9.11E-09	39	0.0341
T1D	SUOX	G ‡	12	56,390,9 64	−5.47	4.49E-08	50	0.1339
T1D	BTN3A2	M	6	26,365,3 87	−5.11	3.30E-07	49	0.7662
T1D	PRSS16	M	6	27,215,4 80	4.83	1.34E-06	31	0.1639
T1D	FAM109A	V	12	111,798, 339	−4.76	1.94E-06	17	0.0665
T1D	SH2B3	G	12	111,843, 752	4.67	3.05E-06	26	0.0368

Evidence: H= HLA-region genes on chromosome 6p21; M=extended Major Histocompatibility Complex; G=Genes previously reported to be associated with disease risk in the NHGRI GWAS catalog excluding studies with WTCCC samples; G‡= reported in studies including WTCCC samples; V= in vicinity of genes of reported gene (1MB).