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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
  1. 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 “*”