Table 1

Genome-wide association studies (GWASs)-associated expression quantitative trait loci (eQTL) affecting gene regulatory elements

#	GWAS-associated QTL variant	Chr	Variant genomic position	Associated disease	Affected DNA regulatory element	Affected gene(s)	Gene TSS genomic position (Refseq)	Genomic distance variant to TSS (bp)	Reference paper
1	rs34481144	11	320 836	Influenza infection	Core promoter	IFITM3	320 813	23	65
2	rs71542466	6	32 666 728	/	Proximal promoter	HLA-DQB1	32 666 607	121	66
3	rs115662534(T)	20	46 117 814	/	Proximal enhancer	CD40	46 118 344	−530	67
3	rs548231435(C)	20	46 118 145	/	Proximal promoter	CD40	46 118 344	−199	67
4	rs4794067	17	47 731 462	Autoimmune hepatitis—related to SLE and periodontitis	Proximal enhancer (?)	TBX21 (Tbet)	47 733 455	−1993	68
5	rs10750836	11	69 048 055	SLE	Proximal promoter/proximal enhancer	TPCN2	69 048 998	−943	69
6	rs2275675	1	183 470 348	SLE	Proximal promoter/proximal enhancer	SMG7	183 472 621	−2273	70
7	rs6426749	1	22 384 980	Osteoporosis	Enhancer	LINC00339	22 025 504	359 476	71
8	rs174575	11	61 830 531	Colorectal cancer	Enhancer	FADS2	61 828 391	2140	72
						AP002754.2	61 655 702	174 829
9	rs56069439	19	17 283 116	Breast cancer and ovarian cancer	Enhancer	ABHD8	17 301 616	−18500	73
10	rs4748812	10	22 550 154	Childhood acute lymphoblastic leukaemia	Enhancer	PIP4K2A	22 714 326	−164172	74
	rs11591377	10	22 124 373	Childhood acute lymphoblastic leukaemia	Enhancer	BMI1	22 326 450	−202077
11	rs62510556	8	117 152 033	Type 2 diabetes	Enhancer	SLC30A8	116 950 217	201 816	75
12	rs7864322 rs12352658 rs7847449 and rs10759944 all in LD with the GWAS variant rs965513	9	97 786 652	Thyroid cancer	All variants in the same enhancer	FOXE1	97 853 915	−67263	76
			97 789 486			FOXE1	97 853 915	−64429
			97 789 616			FOXE1	97 853 915	−64299
			97 794 690			FOXE1	97 853 915	−59225
			97 793 827			FOXE1	97 853 915	−60088
			97 786 652			PTCSC2	97 853 080	−66428
			97 789 486			PTCSC2	97 853 080	−63594
			97 789 616			PTCSC2	97 853 080	−63464
			97 794 690			PTCSC2	97 853 080	−58390
			97 793 827			PTCSC2	97 853 080	−59253
13	rs1335532	1	116 558 335	Protection from multiple sclerosis	Enhancer	CD58	116 570 972	−12637	77
14	rs2159100	12	2 237 227	Schizophrenia	Enhancer	CACNA1C	2 052 987	184 240	78
15	rs3181077	3	46 204 161	Narcolepsy	Enhancer	CCR1	46 208 313	−4152	79
						CCR3	46 163 604	−46163604
16	rs7163757	15	62 099 409	Type 2 diabetes	Enhancer	VPS13C	61 854 457	244 952	80
17	rs148314165	6	137 908 854	SLE	Enhancer	TNFAIP3	137 871 228	37 626	81
	rs200820567		137 908 903			TNFAIP3	137 871 228	37 675
18	rs139767239, rs115133228, rs12722502, rs12722635, in LD with rs706778 and rs706779	10	6 058 827	T1D	Intronic enhancers	IL2RA	6 062 151	−3324	82
			6 054 123				6 062 151	−8028
			6 051 176				6 062 151	−10975
			6 051 177				6 062 151	−10974
			6 056 986				6 062 151	−5165
			6 056 861				6 062 151	−5290
19	rs17810546	3	159 947 262	Coeliac disease	Silencer	IL12A	159 989 057	−41795	83

bp, base pair; Chr, chromosome; SLE, systemic lupus erythematosus; T1D, type 1 diabetes; TSS, transcription start site.