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Table 2 Loci validated or replicated by individual patient TaqMan genotyping

From: A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients

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
  1. 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