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