Table 2 |.
Putative causal variants and coding variants in LD (r2 > 0.5) with index variants in EAS loci
| Varianta | rsID | Subtype | ORb | P b | Gene | AA change | EAS_MAF | EUR_MAF | R2c | PIPd | Tiere |
|---|---|---|---|---|---|---|---|---|---|---|---|
| chr1:67182913:G:A | rs76418789 | IBDf | 0.57 | 2.0E-34 | IL23R | G149R | 0.053 | 0.002 | 1.00 | 1.00 | 1 |
| chr1:154962487:G:A | rs3766920 | CD | 1.46 | 7.3E-13 | SHC1 h | 0.050 | 0.000 | 1.00 | 1.00 | 1 | |
| chr10:62710915:C:T | rs224136 | CD | 0.76 | 5.5E-27 | ADO | 0.303 | 0.182 | 1.00 | 1.00 | 1 | |
| chr19:3548233:A:G | rs2240751 | CD | 1.17 | 5.0E-09 | MFSD12 | Y182H | 0.269 | 0.010 | 1.00 | 0.99 | 1 |
| chr20:63744874:T:C | rs2427537 | CD | 0.71 | 1.2E-11 | ZBTB46 | 0.044 | 0.470 | 0.23 | 0.97 | 1 | |
| chr10:110426390:C:T | rs11195128 | CD | 1.33 | 6.0E-16 | DUSP5 | 0.148 | 0.320 | 1.00 | 0.95 | 2 | |
| chr2:190704810:C:T | rs142152795 | CD | 1.43 | 2.1E-09 | NAB1 | 0.021 | 0.000 | 1.00 | 0.93 | 2 | |
| chr7:74711703:C:T | rs117026326 | CD | 1.37 | 8.9E-11 | GTF2I | 0.073 | 0.016 | 1.00 | 0.91 | 2 | |
| chr16:85976134:T:C | rs16940186 | UC | 1.27 | 8.8E-18 | IRF8 | 0.258 | 0.175 | 1.00 | 0.89 | 2 | |
| chr4:38323415:T:C | rs6856616 | CD | 1.33 | 4.0E-29 | LINC02513 | 0.232 | 0.060 | 0.69 | 0.87 | 2 | |
| chr10:79286696:G:A | rs1250566 | CD | 0.82 | 1.9E-17 | ZMIZ1 | 0.340 | 0.282 | 1.00 | 0.55 | 2 | |
| chr17:39732988:C:CT | rs34372308 | UC | 0.86 | 3.8E-10 | MIEN1 | 0.440 | 0.305 | 1.00 | 0.52 | 2 | |
| chr22:36911669:C:T | rs12628495 | CD | 1.27 | 8.2E-20 | CSF2RB | 0.339 | 0.090 | 1.00 | 0.52 | 2 | |
| chr19:48709897:T:C | rs78966440 | CD | 1.17 | 1.5E-11 | FUT2 | 0.497 | 0.000 | 0.31 | 0.52 | 2 | |
| chr1:161509955:A:G | rs1801274 | UC | 0.84 | 8.5E-11 | FCGR2A | H167R | 0.278 | 0.489 | 0.93 | 0.29 | 2 |
| chr2:240630832:A:C | rs3749172 | IBDg | 0.81 | 6.4E-28 | GPR35 | S325R | 0.289 | 0.440 | 1.00 | 0.11 | 2 |
| chr1:21981045:C:T | rs7528405 | IBD | 1.14 | 2.1E-08 | CELA3B | R79W | 0.245 | 0.008 | 0.98 | - | 3 |
| chr1:24964519:A:T | rs6672420 | CD | 0.86 | 4.6E-10 | RUNX3 | I18N | 0.312 | 0.479 | 0.91 | - | 3 |
| chr1:28150351:G:T | rs5938 | CD | 1.27 | 3.2E-08 | PTAFR | A224D | 0.115 | 0.000 | 0.73 | - | 3 |
| chr1:154968787:G:A | rs8191981 | IBD | 1.32 | 1.6E-08 | SHC1 h | A205V | 0.050 | 0.000 | 1.00 | - | 3 |
| chr2:233274722:A:G | rs2241880 | CD | 1.15 | 3.0E-09 | ATG16L1 | T317A | 0.322 | 0.463 | 0.98 | - | 3 |
| chr7:955367:G:C | rs79805216 | IBD | 0.83 | 2.0E-13 | ADAP1 | P14R | 0.205 | 0.018 | 0.95 | - | 3 |
| chr7:1093055:C:T | rs1133041 | IBD | 0.86 | 1.2E-09 | GPER1 | L349F | 0.158 | 0.013 | 0.53 | - | 3 |
| chr7:1093188:TTC:T | rs3840681 | IBD | 0.86 | 1.2E-09 | GPER1 | FL393-394FX | 0.157 | 0.014 | 0.53 | - | 3 |
| chr12:109953174:T:C | rs925368 | CD | 0.73 | 3.8E-09 | GIT2 | N387S | 0.072 | 0.000 | 0.96 | - | 3 |
| chr13:43883789:A:G | rs3764147 | CD | 1.22 | 1.3E-17 | LACC1 | I254V | 0.347 | 0.227 | 1.00 | - | 3 |
| chr14:87941544:A:G | rs398607 | IBD | 1.15 | 4.6E-09 | GALC | I562T | 0.231 | 0.488 | 0.60 | - | 3 |
| chr14:88011538:A:C | rs3742704 | IBD | 1.19 | 2.8E-12 | GPR65 | I231L | 0.206 | 0.099 | 0.71 | - | 3 |
| chr16:28496323:C:G | rs180743 | CD | 1.27 | 3.9E-12 | APOBR | P428A | 0.104 | 0.348 | 0.78 | - | 3 |
| chr16:28502082:A:G | rs181206 | CD | 1.29 | 5.5E-13 | IL27 | L119P | 0.083 | 0.287 | 0.97 | - | 3 |
| chr16:28592334:T:G | rs1059491 | CD | 1.28 | 7.4E-13 | SULT1A2 | N235T | 0.074 | 0.317 | 0.81 | - | 3 |
| chr16:28595911:A:G | rs1136703 | CD | 1.29 | 3.6E-13 | SULT1A2 | I7T | 0.073 | 0.310 | 0.80 | - | 3 |
| chr17:39727784:C:G | rs1058808 | UC | 1.15 | 9.2E-09 | ERBB2 | P1170A | 0.402 | 0.327 | 0.93 | - | 3 |
| chr17:59886176:A:G | rs1292053 | IBD | 1.11 | 5.6E-09 | TUBD1 | M76T | 0.425 | 0.418 | 1.00 | - | 3 |
| chr19:48751247:G:A | rs2071699 | IBD | 1.13 | 3.2E-10 | FUT1 | A12V | 0.313 | 0.022 | 1.00 | - | 3 |
| chr19:54219486:A:G | rs255774 | CD | 1.23 | 2.4E-08 | LILRB3 | Splice donor | 0.486 | 0.482 | 1.00 | - | 3 |
| chr22:21628603:C:T | rs2298428 | IBD | 1.16 | 4.0E-14 | YDJC | A263T | 0.412 | 0.177 | 1.00 | - | 3 |
| chr22:36875840:T:C | rs2075939 | CD | 0.83 | 1.6E-14 | NCF4 | L272P | 0.318 | 0.164 | 0.50 | - | 3 |
Variant annotated as CHR:POS:A1:A2. CHR, chromosome; POS, genomic position in genome build 38; A1, reference allele; A2, effect allele.
OR and P-value are from the meta-analysis including all EAS samples. P-value is from the inverse-variance-weighted fixed-effect meta-analysis (two-tailed).
R2, LD with the index variant measured as r2 using the 1000 genomes EAS individuals.
PIP, posterior inclusion probability.
Tier, 1 (PIP > 95% in EAS); 2 (PIP > 50%, or PIP > 10% if missense or predicted loss-of-function); 3 (missense variants tagging the index variants with r2 > 0.5).
rs76418789 has PIP = 1 for both CD and UC and was therefore listed as PIP = 1 for IBD.
rs3749172 has PIP = 0.11 and 0.09 for CD and UC, respectively, and was therefore listed as PIP = 0.11 with IBD.
The two SHC1 variants are in incomplete LD in study samples and complete LD in 1000 genomes EAS (rs3766920 has higher significance). We boldfaced variants implicating new IBD loci for tiers 1 and 2, and variants that had not reached genome-wide significance nor been identified as putative causal in previous studies4,5,7,8,12,34–43 for tier 3.