Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Ana Márquez; Martin Kerick; Alexandra Zhernakova; Javier Gutierrez-Achury; Wei-Min Chen; Suna Onengut-Gumuscu; Isidoro González-Álvaro; Luis Rodriguez-Rodriguez; Raquel Rios-Fernández; Miguel A. González-Gay; Maureen D. Mayes; Soumya Raychaudhuri; Stephen S. Rich; Cisca Wijmenga; Javier Martín

doi:10.1186/s13073-018-0604-8

Table 1 Independent genetic variants reaching genome-wide level of significance in the subset-based meta-analysis and showing pleiotropic effects across diseases

From: Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single-disease and cross-phenotype associations

Region	Position (bp)	SNP	Gene	A1	P2sided	Best subset
1p36.32	2,534,978	rs6664969	MMEL1	A	2.86E−10	CeD RA
1p36.13	17,655,407	rs1748041	PADI4	C	3.63E−08	RA SSc
1p13.2	114,377,568	rs2476601	PTPN22	A	6.36E−119	RA T1D
1p13.2	114,388,804	rs1217403	PTPN22	C	4.66E−11	RA* T1D*
1q24.3	172,674,776	rs10912267	FASLG	A	3.90E−09	CeD T1D
2q11.2	100,764,004	rs13415465	AFF3	G	3.72E−12	CeD RA T1D
2q31.3	182,057,640	rs12619531	ITGA4	G	1.18E−18	CeD SSc
2q32.3	191,538,562	rs10931468	NAB1	A	1.56E−08	RA SSc
2q32.3	191,902,184	rs6749371	STAT4	T	3.84E−08	CeD SSc*
2q32.3	191,964,633	rs7574865	STAT4	T	3.16E−09	CeD* RA SSc T1D*
2q33.2	204,612,058	rs7426056	CD28	A	6.68E−12	CeD RA
2q33.2	204,738,919	rs3087243	CTLA4	A	5.08E−16	RA T1D
3p14.3	58,183,636	rs35677470	DNASE1L3	A	1.04E−11	RA SSc
3q25.33	159,647,674	rs17753641	IL12A	G	1.64E−29	CeD SSc*
4p15.2	26,088,128	rs16878091	RBPJ	A	2.53E−12	RA T1D
5q33.1	150,438,988	rs1422673	TNIP1	T	1.87E−09	CeD RA SSc
6q15	90,976,768	rs72928038	BACH2	A	9.34E−12	CeD RA T1D
6q23.3	138,003,822	rs11757201	TNFAIP3	C	1.27E−11	CeD RA T1D
6q23.3	138,243,739	rs58721818	TNFAIP3	T	5.26E−10	RA SSc
6q25.3	159,470,417	rs212407	TAGAP	G	6.74E−14	CeD RA T1D
7p14.1	37,382,465	rs60600003	ELMO1	G	4.25E−13	CeD SSc
7p12.1	51,015,193	rs7780389	COBL	T	2.25E−08	RA T1D
7q32.1	128,572,766	rs4731532	IRF5	A	1.25E−10	RA SSc
9p13.3	34,710,260	rs2812378	CCL21	G	1.04E−09	CeD RA
10p15.1	6,101,713	rs3118470	IL2RA	C	5.92E−09	RA T1D
10p15.1	6,116,254	rs72776098	IL2RA	A	7.10E−10	SSc T1D
10p15.1	6,390,450	rs947474	PRKCQ	G	1.28E−08	CeD RA T1D
10p14	8,102,272	rs3802604	GATA3	G	4.67E−08	RA T1D
10q22.3	81,045,280	rs1250568	ZMIZ1	C	3.87E−15	CeD SSc T1D
11q23.3	118,726,843	rs10892299	DDX6	T	2.25E−13	CeD SSc T1D
12q13.2	56,470,625	rs11171739	IKZF4	C	1.87E−20	RA T1D
15q14	38,828,140	rs8043085	RASGRP1	T	1.53E−08	RA T1D
15q25.1	79,234,957	rs34593439	CTSH	A	1.47E−14	CeD T1D
17q12	38,033,277	rs1054609	ORMDL3	C	3.70E−08	RA SSc T1D
18p11.21	12,777,573	rs2542148	PTPN2	C	5.11E−16	CeD T1D
19p13.2	10,427,721	rs74956615	TYK2	A	1.62E−17	RA SSc T1D
21q22.3	43,855,067	rs1893592	UBASH3A	C	4.86E−12	CeD T1D
22q11.1	21,936,152	rs66534072	YDJC	G	2.05E−08	CeD SSc

The selected lead SNP in each region is shown, together with the best subset obtained from the subset-based meta-analysis. Position (bp), base pair position in hg19; SNP, single nucleotide polymorphism; Gene, annotated gene as described in methods; A1, alternative allele used in the logistic regression; P2sided, p value from the two-sided subset-based meta-analysis; Best subset, phenotypes contributing to the association signal. Diseases included in the best subset and for which identified associations have not been previously reported are shown in bold; novel signals within known risk loci are indicated by “*”

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