Table 3. Nominally (p < 0.05) replicated CD risk loci.
| p values | Odds ratios | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Chr | Critical region | Scan | Replication | Combined | Num. genes | Gene of interest | RAF | Risk allele | Case Ctrl | TDT |
| rs4807569 | 19p13 | 1.05 -1.15 | 1.16×10-8 | 0.00347 | 2.12×10-9 | 2 | 0.217 | C | 1.02 | 1.26 | |
| rs780094 | 2p23 | 27.30 - 27.77 | 3.82×10-6 | 0.00381 | 3.14×10-7 | 22 | GCKR | 0.397 | T | 1.08 | 1.13 |
| rs3763313 | 6p21 | 32.44-32.79 * | 1.45×10-8 | 0.00602 | 5.20×10-9 | 7 | BTNL2, DRA, DRB, DQA | 0.188 | C | 1.19 | 1.01 |
| rs13003464 | 2p16 | 61.09 - 61.14 | 3.44×10-5 | 0.00565 | 4.60×10-6 | 1 | CCDC139 | 0.376 | G | 1.16 | 1.08 |
| rs991804 | 17q12 | 29.57 - 29.70 | 4.02×10-6 | 0.0135 | 1.07×10-6 | 4 | CCL2, CCL7 | 0.726 | C | 1.1 | 1.08 |
| rs12529198 | 6p25 | 5.04 - 5.11 | 7.08×10-7 | 0.0192 | 6.96×10-7 | 1 | LYRM4 | 0.062 | G | 1.12 | 1.19 |
| rs17309827 | 6p25 | 3.36 - 3.42 | 2.08×10-6 | 0.0391 | 2.74×10-6 | 1 | SLC22A23 | 0.639 | T | 1.1 | 1.02 |
| rs7758080 | 6q25 | 149.54 - 149.65 | 7.28×10-6 | 0.044 | 8.78×10-6 | 0 | 0.274 | G | 1.12 | 0.99 | |
| rs8098673 | 18q11 | 17.74 - 17.93 | 3.18×10-5 | 0.0443 | 2.88×10-5 | 0 | 0.329 | C | 1.05 | 1.09 | |
| rs917997 | 2q11 | 102.31 - 102.64 | 2.16×10-5 | 0.0493 | 2.22×10-5 | 5 | IL18RAP | 0.222 | T | 1.05 | 1.11 |
RAF is risk allele frequency in control samples (see Supplementary Table 5 for details). Critical region is in NCBI B35 coordinates, with definition as described in Methods. Risk alleles are defined relative to the + strand of the reference.
*
SNPs with p<0.0001 were observed throughout the MHC from 30.2 – 32.9 Mb but only this largest signal from the region was followed up. More detailed study of the MHC will be required to identify and localize potentially independent signals from this region.