Table 2.
Loci validated or replicated by individual patient TaqMan genotyping
| Locus | SNP | Position | Location | Putative (nearby) gene(s) | PBC | PSC | MA, MAF | ||
|---|---|---|---|---|---|---|---|---|---|
| P-value | OR | P-value | OR | ||||||
| 1p32 | rs4927257 | 56046320 | prom. | 0.033 | 0.83 | 0.026 | 0.72 | A, 0.439 | |
| 2p25.3 | rs1965732 | 3709108 | intron | ALLC | 0.028 | 1.24 | 0.029 | 1.41 | G, 0.266 |
| 5q34 | rs9686714 | 167853274 | intron | WWC1 | 0.048 | 0.68 | 7.7E-4 | 0.195 | C, 0.066 |
| 6p21 | rs2187668 | 32605884 | intron | HLA-DQA1 | 0.021 | 0.73 | 1.53E-7 | 2.47 | T, 0.128 |
| 6p21 | rs9272346 | 32604372 | prom. | HLA-DQA1 | 0.0067 | 0.79 | 0.025 | 1.37 | G, 0.422 |
| 6p21 | rs7775228 | 32658079 | inter. | LOC100294145, C4B_2 | 7.94E-9 | 1.84 | 0.00171 | 0.46 | C, 0.146 |
| 6p21 | rs3213489 | 32724305 | intron | HLA-DQB2 | 8.37E-9 | 0.60 | 0.00155 | 1.56 | T, 0.416 |
| 6p21 | rs1799908 | 33144243 | intron | COL11A2 | 0.032 | 1.21 | 0.0045 | 0.63 | A, 0.405 |
| 6p21 | rs7454108 | 32681483 | inter. | LOC100294145, C4B_2 | 0.0090 | 1.43 | 0.00130 | 0.326 | C, 0.086 |
| 9q34.3 | rs10119096 | 139801932 | intron | TRAF2 | 0.00087 | 0.70 | 0.041 | 0.70 | T, 0.263 |
| 10q26.11 | rs17098094 | 120592334 | inter. | MIR4681, CACUL1 | 0.0174 | 0.81 | 0.032 | 0.73 | G, 0.394 |
| 1p31.3 | rs10489626 | 67793171 | intron | IL12RB2 | 2.11E-5 | 1.59 | G, 0.179 | ||
| rs3790567 | 67822377 | intron | IL12RB2 | 8.4E-4 | 1.37 | A, 0.242 | |||
| 1q32.1 | rs3024505 | 206939904 | inter. | IL24, CTSE | 0.047 | 1.25 | A, 0.158 | ||
| 2q31.1 | rs2287619 | 169836730 | intron | ABCB11 | 0.0079 | 1.50 | C, 0.076 | ||
| 1q24.3 | rs12118836 | 171256038 | inter. | MIR3120, MIR1295A | 0.0081 | 1.37 | A, 0.145 | ||
| 3q13 | rs28413019 | 109890863 | inter. | PVRL3-AS1, DPPA2 | 0.022 | 1.25 | G, 0.237 | ||
| rs1491590 | 70657915 | inter. | MIR1284, MITF | 0.0021 | 1.34 | G, 0.251 | |||
| 4p15.1 | rs13126571 | 27725689 | inter. | TBC1D19 | 0.031 | 1.24 | A, 0.230 | ||
| 4p14 | rs3114381 | 40533297 | intron | RBM47 | 0.0123 | 1.28 | T, 0.232 | ||
| 4q26 | rs979961 | 117850456 | inter. | TRAM1L1, MIR1973 | 0.0062 | 1.39 | C, 0.131 | ||
| 6p21 | rs9268979 | 32435044 | inter. | LOC100294145, C4B_2 | 6.73E-6 | 0.68 | T, 0.471 | ||
| 6p21 | rs3128927 | 33074288 | inter. | MIR1275, LOC100294145 | 2.16E-5 | 1.50 | T, 0.240 | ||
| 6q27 | rs4710185 | 167522386 | intron | CCR6 | 0.020 | 1.23 | A, 0.358 | ||
| 6q27 | rs9459874 | 167504127 | intron | CCR6 | 0.0040 | 1.29 | T, 0.425 | ||
| 6q27 | rs975822 | 167516458 | intron | CCR6 | 0.0042 | 1.29 | T, 0.459 | ||
| 7q32.1 | rs10488631 | 128594183 | inter. | SMKR1, LOC100130705 | 0.0023 | 1.43 | C, 0.132 | ||
| 7p14.3 | rs965571 | 33622588 | intron | BBS9 | 7.0E-4 | 1.43 | C, 0.207 | ||
| 11q12.3 | rs35730843 | 62527634 | prom. | POLR2G | 1.21E-5 | 0.393 | C, 0.070 | ||
| 11p15.3 | rs12786216 | 11275192 | inter. | MIR4299, MRVI1-AS1 | 0.0076 | 0.77 | C, 0.299 | ||
| 11q23.3 | rs11217040 | 118680648 | inter. | LOC100131626 | 9.22E-5 | 0.66 | A, 0.246 | ||
| 11q24.3 | rs73022813 | 130704378 | inter. | SNX19, ADAMTS8 | 0.043 | 1.24 | A, 0.176 | ||
| 12p13.31 | rs7975557 | 9853697 | inter. | KLRF2, MIR1244-1 | 0.042 | 1.54 | T, 0.035 | ||
| 14q21.1 | rs10083358 | 39001998 | inter. | LOC100288846, MIPOL1 | 0.0026 | 1.34 | G, 0.252 | ||
| 16p12.3 | rs8055224 | 20285401 | inter. | ERI2, IQCK | 0.0077 | 0.54 | G, 0.050 | ||
| 16q23.3 | rs8049648 | 83217488 | intron | CDH13 | 0.00175 | 1.68 | C, 0.061 | ||
| 19q13.33 | rs3745516 | 50926742 | intron | SPIB | 7E-05 | 1.45 | A, 0.254 | ||
| 21q22.11 | rs7279062 | 32074387 | inter. | KRTAP21-3, KRTAP25-1 | 0.0110 | 0.80 | T, 0.476 | ||
| 17q12 | rs9303277 | 37976469 | intron | IKZF3 | 0.0051 | 1.27 | T, 0.478 | ||
| 3q22.1 | rs11917172 | 132166266 | coding | DNAJC13 | 0.0122 | 0.53 | G, 0.138 | ||
| 4p16.1 | rs7686718 | 10171487 | inter. | CLNK, USP17L10 | 0.00161 | 1.63 | C, 0.261 | ||
| 6q12 | rs13191240 | 69675459 | intron | ADGRB3 | 0.0095 | 0.2 | C, 0.04 | ||
| 5p15.31 | rs6869702 | 6401135 | inter. | MIR4278, ICE1 | 0.047 | 0.74 | G, 0.409 | ||
| 5q22.2 | rs1554624 | 111655382 | intron | EPB41L4A | 0.0126 | 0.55 | G, 0.154 | ||
| 5q34 | rs3822659 | 167858372 | coding | WWC1 | 0.0051 | 0.24 | TG, 0.053 | ||
| 6p21 | rs3130484 | 31715882 | intron | MSH5-SAPCD1 | 5.12E-11 | 3.23 | C, 0.101 | ||
| 6p21 | rs1264377 | 30764907 | inter. | PSORS1C3, MIR877 | 8.02E-8 | 2.39 | A, 0.159 | ||
| 6p21 | rs2524163 | 31259579 | intron | HLA-B | 5.94E-7 | 2.02 | C, 0.429 | ||
| 6p21 | rs3130626 | 31598489 | intron | PRRC2A | 1.5E-6 | 2.10 | G, 0.207 | ||
| 6p21 | rs419788 | 31928799 | intron | SKIV2L | 1.21E-6 | 2.03 | T, 0.250 | ||
| 6p22.1 | rs3815081 | 30114074 | intron | TRIM40 | 0.0141 | 0.59 | G, 0.169 | ||
| rs1936365 | 28268452 | intron | PGBD1 | 0.0034 | 1.72 | C, 0.128 | |||
| 11q24.3 | rs34708188 | 128223560 | inter. | SENCR | 0.0057 | 2.27 | T, 0.038 | ||
| 7q35 | rs954072 | 144757945 | inter. | CTAGE4 | 0.0069 | 0.66 | C, 0.406 | ||
| 8q21.13 | rs1380634 | 80237893 | inter. | MIR5708, LOC101241902 | 0.001011 | 1.70 | G, 0.241 | ||
| 15q21.3 | rs11853454 | 54169638 | inter. | UNC13C, WDR72 | 0.040 | 1.39 | A, 0.218 | ||
| 17p13.2 | rs238224 | 4863410 | intron | SPAG7 | 0.0174 | 0.57 | A, 0.146 | ||
Map loci refer to the GRCh37 assembly. SNPs chosen on the basis of Celiac disease and IBD association are bolded. Odds ratios (ORs) are for minor alleles. SNP single nucleotide polymorphism, MA minor allele, MAF minor allele frequency; inter., intergenic (location); prom., promoter