Table 1.

Twenty-seven independent loci reaching genome-wide significance (P_META < 5 × 10⁻⁸) after adjustment for the use of shared controls using an inverse χ² meta-analysis across the pAIDs

Chr	Pos (Mb)	SNP	Region	Gene	A1	MAF	PMETA	Known P*	pAIDs
1	67.7	rs11580078	1p31.3	IL23R	G	0.43	8.4 × 10−11	1.0 × 10−146	CD#
1	82.2	rs2066363	1p31.1	ADGRL2	C	0.34	8.4 × 10−11	Novel	CVID, JIA
1	114.3	rs6679677	1p13.2	PTPN22	A	0.09	8.4 × 10−11	1.1 × 10−88	THY#, PSOR, T1D#, JIA#
2	234.2	rs36001488	2q37.1	ATG16L1	C	0.48	8.4 × 10−11	1.0 × 10−12	PSOR, CD#
3	49.6	rs4625	3p21.31	DAG1	G	0.31	8.4 × 10−11	1.0 × 10−47	PSOR#, CEL, UC#, CD#
4	123.6	rs62324212	4q27	IL21	A	0.42	2.6 × 10−8	1.0 × 10−9	THY, AS, CEL#, CVID, UC#, T1D#, JIA#, CD#
4	183.7	rs7660520	4q35.1	TENM3	A	0.26	8.4 × 10−11	Novel	THY, AS, CEL, SLE, CVID, JIA
5	40.5	rs7725052	5p13.1	PTGER4	C	0.43	8.4 × 10−11	1.4 × 10−10	CD#
5	55.4	rs7731626	5q11.2	ANKRD55	A	0.39	1.4 × 10−10	2.7 × 10−11	JIA#, CD#
5	131.8	rs11741255	5q31.1	IL5	A	0.42	1.6 × 10−9	1.4 × 10−52	PSOR#, CEL, CD#
5	158.8	rs755374	5q33.3	IL12B	T	0.32	2.3 × 10−10	1.4 × 10−42	AS#, CEL, UC#, CD#
9	117.6	rs4246905	9q32	TNFSF15	T	0.28	9.5 × 10−9	1.2 × 10−17	UC#, CD#
9	139.3	rs11145763	9q34.3	CARD9	C	0.40	3.3 × 10−8	1.0 × 10−6	AS#, UC#, CD#
10	6.1	rs706778	10p15.1	IL2RA	T	0.41	6.3 × 10−9	1.7 × 10−12	THY, AS, PSOR#, CEL, T1D#, JIA#
10	37.6	rs7100025	10p11.21	ANKRD30A	G	0.34	8.4 × 10−11	Novel	JIA
10	64.4	rs10822050	10q21.2	ZNF365	C	0.39	8.4 × 10−11	5.0 × 10−17	SLE, CD#
10	81.0	rs1250563	10q22.3	ZMIZ1	C	0.29	1.3 × 10−8	1.1 × 10−30	PSOR#, CD#
10	101.3	rs1332099	10q24.2	NKX2-3	T	0.46	9.1 × 10−11	1.0 × 10−54	UC#, CD#
11	2.2	rs17885785	11p15.5	INS	T	0.20	8.4 × 10−11	4.4 × 10−48	T1D#
12	40.8	rs17466626	12q12	LRRK2	G	0.02	3.2 × 10−10	3.0 × 10−10	AS, CD#
12	56.4	rs1689510	12q13.2	SUOX	C	0.31	4.0 × 10−9	1.1 × 10−10	PSOR#, T1D#
15	67.5	rs72743477	15q22.33	SMAD3	G	0.21	8.4 × 10−11	2.7 × 10−19	AS, UC, CD#
16	28.3	rs12598357	16p11.2	SBK1	G	0.39	4.4 × 10−9	1.0 × 10−8	THY, AS#, PSOR, CEL, UC, CD#
16	50.3	rs77150043	16q12.1	ADCY7	T	0.23	6.0 × 10−9	Novel	PSOR, CD
16	50.7	rs117372389	16q12.1	NOD2	T	0.02	8.4 × 10−11	2.9 × 10−69	CD#
21	40.5	rs2836882	21q22.2	PSMG1	A	0.27	4.8 × 10−8	2.8 × 10−14	UC#, CD#
23	135.7	rs2807264	Xq26.3	CD40LG	C	0.21	1.3 × 10−8	Novel	CEL, UC, CD

Chr, chromosome; Pos (Mb), position in hg19; Region, cytogenetic band; A1, alternative allele; MAF, minor allele frequency (controls);

Known P*, lowest P value from published association studies.

Pound symbols (#) denote previously reported disease-associated SNPs.

“Novel” denotes new loci (bolded) that reached genome-wide significance for the first time in the present study (to our knowledge).