Table 1. Expression quantitative trait locus (eQTL) analysis results between SNPs and the expressions of 11 genes from the 108 “identified” genes.

SNP ID	Chr.	Location	Allele	Role	Association P-value	Gene 1	Gene 2	Implicated Gene	eQTL gene	Effect	Score	Target	Ref.
rs4728142	chr7	128573967	A/G	unknown	8.00E-19	KCP	IRF5	IRF5	IRF5	eqtl	130.5	Monocytes	[18]
										eqtl	8.6	LCLs	[20]
rs1573649	chr6	32731258	C/T	5′utr	2.00E-10	HLA-DQB2	HLA-DQB2	HLA-DQB2	HLA-DQB2	PP-eqtl	0.1	LCLs	[19]
rs6903130	chr6	32732210	A/G	upstream	4.43E-10	HLA-DQB2	HLA-DQB2	HLA-DQB2	HLA-DQB2	PP-eqtl	0	LCLs	[19]
rs16898264	chr6	32677152	A/G	unknown	3.85E-09	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DQB1	exonQTL	4.4	LCLs	[22]
										transcriptQTL	4	LCLs	[22]
rs2647012	chr6	32664458	A/G	unknown	1.27E-13	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DQB1	exonQTL	6.9	LCLs	[22]
										transcriptQTL	5.6	LCLs	[22]
rs2647050	chr6	32669767	C/T	unknown	5.38E-09	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DQB1	exonQTL	4.4	LCLs	[22]
										transcriptQTL	4	LCLs	[22]
rs2856717	chr6	32670308	C/T	unknown	1.03E-13	HLA-DQB1	HLA-DQA2	N/A	HLA-DQB1	eqtl	33.9	Monocytes	[18]
										exonQTL	6.3	LCLs	[22]
										transcriptQTL	4.8	LCLs	[22]
rs2856718	chr6	32670255	A/G	unknown	5.33E-09	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DQB1	exonQTL	4.4	LCLs	[22]
										transcriptQTL	4.1	LCLs	[22]
rs2856725	chr6	32666738	A/G	unknown	1.11E-13	HLA-DQB1	HLA-DQA2	N/A	HLA-DQB1	exonQTL	6.4	LCLs	[22]
										transcriptQTL	4.9	LCLs	[22]
rs2858305	chr6	32670464	A/C	unknown	7.88E-14	HLA-DQB1	HLA-DQA2	N/A	HLA-DQB1	exonQTL	6.8	LCLs	[22]
										transcriptQTL	5.3	LCLs	[22]
rs9275572	chr6	32678999	A/G	unknown	6.41E-14	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DQB1	eqtl	24.3	Monocytes	[18]
										exonQTL	7.1	LCLs	[22]
										transcriptQTL	5.7	LCLs	[22]
rs9275596	chr6	32681631	C/T	unknown	3.33E-16	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DQB1	exonQTL	5.3	LCLs	[22]
										transcriptQTL	4.2	LCLs	[22]
rs2187668	chr6	32605884	A/G	intron	6.00E-28	HLA-DQA1	HLA-DQA1	HLA-DQB2	HLA-DQA1	eqtl	34.6	Monocytes	[18]
										exonQTL	4.3	LCLs	[22]
rs9271100	chr6	32576478	C/T	unknown	1.00E-12	HLA-DRB1	HLA-DQA1	N/A	HLA-DQA1	exonQTL	7.8	LCLs	[22]
										transcriptQTL	5.4	LCLs	[22]
rs3094061	chr6	30321189	G/T	unknown	1.24E-09	HLA-N	UBQLN1P1	IER3	HLA-H	eqtl	33.6	Monocytes	[18]
rs9271100	chr6	32576478	C/T	unknown	1.00E-12	HLA-DRB1	HLA-DQA1	N/A	HLA-DRB1	exonQTL	15.2	LCLs	[22]
										transcriptQTL	10.5	LCLs	[22]
rs2647012	chr6	32664458	A/G	unknown	1.27E-13	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DRA	transcriptQTL	4.5	LCLs	[22]
rs7192	chr6	32411646	G/T	missense	2.02E-10	HLA-DRA	HLA-DRA	HLA-DRA	HLA-DRA	transcriptQTL	9	LCLs	[22]
rs9268832	chr6	32427789	C/T	unknown	1.53E-10	HLA-DRB9	HLA-DRB9	HLA-DRA	HLA-DRA	transcriptQTL	9.5	LCLs	[22]
rs9275224	chr6	32659878	A/G	unknown	4.45E-12	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DRA	transcriptQTL	4	LCLs	[22]
rs9275572	chr6	32678999	A/G	unknown	6.41E-14	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DRA	eqtl	40.1	Monocytes	[18]
										transcriptQTL	5.1	LCLs	[22]
rs9275596	chr6	32681631	C/T	unknown	3.33E-16	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DRA	transcriptQTL	4.7	LCLs	[22]
rs2647012	chr6	32664458	A/G	unknown	1.27E-13	HLA-DQB1	HLA-DQA2	HLA-DRA	HLA-DQA2	transcriptQTL	4.2	LCLs	[22]
rs2856725	chr6	32666738	A/G	unknown	1.11E-13	HLA-DQB1	HLA-DQA2	N/A	HLA-DQA2	transcriptQTL	4.2	LCLs	[22]
rs2858305	chr6	32670464	A/C	unknown	7.88E-14	HLA-DQB1	HLA-DQA2	N/A	HLA-DQA2	transcriptQTL	4.1	LCLs	[22]
rs9271100	chr6	32576478	C/T	unknown	1.00E-12	HLA-DRB1	HLA-DQA1	N/A	HLA-DRB1	eqtl	93	LCLs	Database#
rs13277113	chr8	11349186	A/G	unknown	1.00E-10	FAM167A	BLK	BLK	FAM167A	exonQTL	6.4	LCLs	[22]
										transcriptQTL	6.5	LCLs	[22]
rs12176317	chr6	26372786	A/G	intron	6.83E-10	BTN3A2	BTN3A2	TRIM38	BTN3A2	eqtl	21.4	LCLs	[19]
										exonQTL	4.8	LCLs	[22]
										PP-eqtl	0	LCLs	[19]
										transcriptQTL	10	LCLs	[22]
rs9379858	chr6	26367689	C/T	intron	6.21E-10	BTN3A2	BTN3A2	TRIM38	BTN3A2	eqtl	21.4	LCLs	20]
										PP-eqtl	0	LCLs	20]
rs9379859	chr6	26369549	C/T	intron	3.79E-10	BTN3A2	BTN3A2	TRIM38	BTN3A2	eqtl	21.4	LCLs	20]
										exonQTL	8.4	LCLs	[22]
										PP-eqtl	0	LCLs	20]
										transcriptQTL	10	LCLs	[22]
rs2618476	chr8	11352541	C/T	intron	2.00E-08	BLK	BLK	BLK	BLK	eqtl	57.1	LCLs	Database#

Note: N/A:not available; “Score”: −log10 (P); LCLs: lymphoblastoid cell lines; transcript-QTL: transcript expression levels against SNPs; exon-QTL: quantified reads for known exons by RNA sequencing against SNPs; sQTL: splicing QTL; PP-eqtl: posterior probability-eqtl.

All the eqtls have cis-effects.

Database#: http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl.

“Gene 1” and “Gene 2”are the nearby genes physically located at two sides of SNP.

“GRAIL P-value “and “Implicated gene” are the results from Gene Relationships Across Implicated Loci (GRAIL) analyses.