Table 5.

VEGAS Results for the 15 Most Significant Genes from Immunochip Analysis on LS and non-LS (48,740 SNPs and 6,840 Genes)

CHR	Gene	nSNPs	Start Position	Stop Position	Test Statistic	P Value	Best SNP	SNP P Value
LS vs. HC
6	TNXB	50	32116910	32185129	1206.77	1.00E-06	rs3130288	6.47E-34
6	CREBL1	51	32191022	32203995	1409.21	1.00E-06	rs3130288	6.47E-34
6	FKBPL	49	32204461	32206045	1464.31	1.00E-06	rs3130288	6.47E-34
6	PRRT1	61	32224117	32227698	2290.62	1.00E-06	rs3130288	6.47E-34
6	PPT2	68	32229278	32239430	2779.84	1.00E-06	rs3130288	6.47E-34
6	EGFL8	69	32240382	32244040	2728.04	1.00E-06	rs3130288	6.47E-34
6	AGPAT1	84	32243966	32253820	3085.42	1.00E-06	rs3130288	6.47E-34
6	C6orf10	149	32368452	32447634	5678.59	1.00E-06	rs3129927	1.82E-33
6	BTNL2	109	32470490	32482878	3946.51	1.00E-06	rs3129927	1.82E-33
6	HLA-DRB1	2	32654524	32665540	144.87	1.00E-06	rs2187668	2.79E-33
6	HLA-DQA1	2	32713160	32719407	288.31	1.00E-06	rs2187668	2.79E-33
6	HLA-DQB1	2	32735634	32742444	288.31	1.00E-06	rs2187668	2.79E-33
6	HLA-DRA	61	32515624	32520802	2278.93	1.00E-06	rs3135394	1.41E-32
6	C2	50	32003472	32021427	1027.18	1.00E-06	rs389884	3.84E-32
6	CFB	45	32021699	32027840	831.90	1.00E-06	rs389884	3.84E-32
Non-LS vs. HC
6	HLA-DRA	61	32515624	32520802	671.61	1.00E-06	rs3129882	5.33E-10
6	BTNL2	109	32470490	32482878	935.64	1.00E-06	rs3129882	5.33E-10
6	HLA-DRB1	2	32654524	32665540	36.76	1.00E-06	rs3830135	2.74E-08
10	ANXA11	6	81904859	81955308	82.55	1.00E-06	rs1049550	1.07E-07
10	PLAC9	3	81882237	81894764	60.30	1.00E-06	rs1049550	1.07E-07
6	HLA-DPB1	58	33151737	33162954	363.18	9.40E-05	rs9277357	1.61E-05
18	PTPN2	54	12775479	12874334	317.12	9.70E-05	rs2852151	1.55E-04
6	HLA-DPA1	46	33140771	33149356	326.14	1.28E-04	rs9277357	1.61E-05
12	PAH	2	1.02E+08	1.02E+08	18.94	1.85E-04	rs2242381	1.10E-04
6	LST1	61	31661949	31664665	249.78	2.11E-04	rs2239704	1.53E-05
6	TNF	60	31651328	31654091	297.74	2.92E-04	rs2239704	1.53E-05
6	LTB	61	31656314	31658181	269.43	3.19E-04	rs2239704	1.53E-05
6	NCR3	60	31664650	31668741	225.25	3.71E-04	rs2239704	1.53E-05
6	PSMB9	87	32929915	32935606	357.37	4.05E-04	rs3819717	2.43E-06
6	PSMB8	87	32916471	32920690	357.37	4.25E-04	rs3819717	2.43E-06

Definition of abbreviations: CHR = chromosome; HC = healthy control subjects; LS = Löfgren’s syndrome; nSNPs = number of SNPs included within a gene; SNP = single-nucleotide polymorphism; VEGAS = Versatile Gene-based Association Study.

The entire lists of LS and non-LS genic SNPs at nominal P < 0.05 are provided in Tables E7 and E8, respectively.