Table 5.
List of Fine-Mapped Credible Variants That Are Near Regulatory Sites Based on Ensembl Variation Annotation
| Lead SNP | Credible SNP | Biotype | CHR | BP | EA | OA | EAF | GWAS |
||
|---|---|---|---|---|---|---|---|---|---|---|
| IBS subtype | OR (95% CI) | P | ||||||||
|
rs6899057 ADCY2 |
rs4286635 | Enhancer | 5 | 7242559 | A | C | 0.60 | IBS | 0.94 (0.92–0.96) | 2.0E-08 |
| rs4286635 | Enhancer | 5 | 7242559 | A | C | 0.60 | IBS-M | 0.92 (0.90–0.94) | 4.1E-08 | |
| rs7718889 | CTCF binding site | 5 | 7200526 | A | T | 0.63 | IBS | 0.94 (0.92–0.96) | 2.1E-08 | |
| rs7718889 | CTCF binding site | 5 | 7200526 | A | T | 0.63 | IBS-M | 0.92 (0.90–0.94) | 2.1E-08 | |
|
rs2048419 CLDN23 / MFHAS1 |
rs1039915 | Enhancer | 8 | 8679614 | T | C | 0.53 | IBS-M | 1.07 (1.05–1.09) | 2.3E-07 |
| rs1039916 | Enhancer | 8 | 8685854 | A | G | 0.52 | IBS-M | 1.07 (1.05–1.09) | 2.7E-07 | |
| rs1039917 | Enhancer | 8 | 8718850 | A | G | 0.37 | IBS-M | 0.93 (0.91–0.95) | 9.6E-07 | |
| rs11775523 | Enhancer | 8 | 8679176 | A | G | 0.53 | IBS-M | 1.07 (1.05–1.09) | 2.7E-07 | |
| rs11992186 | CTCF binding site | 8 | 8524474 | C | G | 0.49 | IBS-M | 1.07 (1.05–1.09) | 1.4E-06 | |
| rs13270070 | Enhancer | 8 | 8691622 | A | T | 0.44 | IBS-M | 0.93 (0.91–0.95) | 1.4E-06 | |
| rs13282015 | Enhancer | 8 | 8659675 | T | G | 0.76 | IBS-M | 0.92 (0.88–0.96) | 3.4E-06 | |
| rs2409092 | Enhancer | 8 | 8682192 | A | T | 0.53 | IBS-M | 1.07 (1.05–1.09) | 1.5E-07 | |
| rs332039 | Enhancer | 8 | 8723651 | C | G | 0.57 | IBS-M | 1.07 (1.05–1.09) | 1.8E-06 | |
| rs35039922 | Enhancer | 8 | 8675325 | A | T | 0.53 | IBS-M | 1.07 (1.05–1.09) | 2.4E-07 | |
| rs35900578 | Enhancer | 8 | 8719513 | A | G | 0.40 | IBS-M | 0.93 (0.91–0.95) | 4.7E-07 | |
| rs3789843 | Enhancer | 8 | 8724257 | T | C | 0.41 | IBS-M | 0.93 (0.91–0.95) | 3.7E-07 | |
| rs3789845 | Enhancer | 8 | 8723918 | T | G | 0.34 | IBS-M | 0.93 (0.91–0.95) | 1.0E-06 | |
| rs3789849 | Enhancer | 8 | 8687054 | C | G | 0.43 | IBS-M | 0.93 (0.91–0.95) | 3.0E-07 | |
| rs3827806 | Enhancer | 8 | 8724276 | T | C | 0.41 | IBS-M | 0.93 (0.91–0.95) | 3.8E-07 | |
| rs4840362 | Enhancer | 8 | 8670082 | C | G | 0.46 | IBS-M | 0.93 (0.91–0.95) | 1.4E-07 | |
| rs4841040 | Promoter | 8 | 8654527 | T | C | 0.53 | IBS-M | 1.08 (1.06–1.10) | 7.8E-08 | |
| rs4841042 | Enhancer | 8 | 8664622 | A | G | 0.46 | IBS-M | 0.93 (0.91–0.95) | 1.4E-07 | |
| rs4841051 | Enhancer | 8 | 8685646 | T | C | 0.52 | IBS-M | 1.07 (1.05–1.09) | 2.2E-07 | |
| rs560544 | CTCF binding site | 8 | 8637429 | A | G | 0.52 | IBS-M | 1.07 (1.05–1.09) | 3.7E-07 | |
| rs56367294 | Enhancer | 8 | 8722527 | A | G | 0.32 | IBS-M | 0.93 (0.89–0.97) | 1.4E-06 | |
| rs60315134 | Enhancer | 8 | 8670599 | A | G | 0.54 | IBS-M | 1.07 (1.05–1.09) | 1.9E-07 | |
| rs7820146 | Enhancer | 8 | 8699757 | A | T | 0.44 | IBS-M | 0.93 (0.91–0.95) | 6.1E-07 | |
| rs7823757 | Enhancer | 8 | 8670177 | A | T | 0.46 | IBS-M | 0.93 (0.91–0.95) | 1.6E-07 | |
| rs7833171 | Enhancer | 8 | 8699761 | T | C | 0.44 | IBS-M | 0.93 (0.91–0.95) | 5.8E-07 | |
| rs882462 | Enhancer | 8 | 8678530 | A | G | 0.47 | IBS-M | 0.93 (0.91–0.95) | 3.5E-07 | |
|
rs2035380 BMAL1 |
rs10766064 | Open chromatin region | 11 | 13277932 | A | G | 0.74 | IBS | 0.94 (0.92–0.96) | 5.7E-07 |
| rs10766065 | Open chromatin region | 11 | 13277961 | T | C | 0.72 | IBS | 0.94 (0.92–0.96) | 9.4E-07 | |
| rs10766066 | Open chromatin region | 11 | 13278027 | A | G | 0.72 | IBS | 0.94 (0.92–0.96) | 9.4E-07 | |
| rs10832018 | Enhancer | 11 | 13312424 | A | G | 0.71 | IBS | 0.94 (0.92–0.96) | 8.9E-08 | |
| rs10832021 | Enhancer | 11 | 13324530 | A | G | 0.71 | IBS | 0.94 (0.92–0.96) | 5.2E-07 | |
| rs11022733 | Enhancer | 11 | 13281557 | A | C | 0.71 | IBS | 0.94 (0.92–0.96) | 8.3E-07 | |
| rs11022734 | Enhancer | 11 | 13281580 | A | G | 0.29 | IBS | 1.06 (1.04–1.08) | 8.3E-07 | |
| rs11022735 | Enhancer | 11 | 13292727 | A | C | 0.30 | IBS | 1.06 (1.04–1.08) | 7.8E-08 | |
| rs11022743 | Promoter | 11 | 13297800 | A | G | 0.27 | IBS | 1.06 (1.04–1.08) | 5.7E-07 | |
| rs11022753 | CTCF binding site | 11 | 13310854 | T | C | 0.73 | IBS | 0.94 (0.92–0.96) | 7.8E-07 | |
| rs11022754 | Enhancer | 11 | 13313243 | A | G | 0.27 | IBS | 1.06 (1.04–1.08) | 7.3E-07 | |
| rs11022756 | Enhancer | 11 | 13315439 | A | C | 0.29 | IBS | 1.06 (1.04–1.08) | 8.9E-08 | |
| rs11022757 | Enhancer | 11 | 13322580 | A | G | 0.29 | IBS | 1.06 (1.04–1.08) | 5.5E-07 | |
| rs11605776 | Enhancer | 11 | 13318524 | A | C | 0.71 | IBS | 0.94 (0.92–0.96) | 4.1E-07 | |
| rs12290622 | Enhancer | 11 | 13314307 | A | G | 0.71 | IBS | 0.94 (0.92–0.96) | 8.5E-08 | |
| rs12361893 | Promoter | 11 | 13301114 | C | G | 0.30 | IBS | 1.06 (1.04–1.08) | 1.5E-07 | |
| rs1351525 | Promoter | 11 | 13301548 | A | T | 0.29 | IBS | 1.06 (1.04–1.08) | 1.5E-07 | |
| rs1384030 | Enhancer | 11 | 13292909 | T | C | 0.30 | IBS | 1.06 (1.04–1.08) | 8.3E-08 | |
| rs1481891 | CTCF binding site | 11 | 13310718 | T | C | 0.29 | IBS | 1.06 (1.04–1.08) | 8.7E-08 | |
| rs1481892 | Promoter | 11 | 13301921 | C | G | 0.71 | IBS | 0.94 (0.92–0.96) | 1.5E-07 | |
| rs2035380 | Enhancer | 11 | 13284345 | T | C | 0.30 | IBS | 1.07 (1.04–1.09) | 3.1E-08 | |
| rs2219998 | Enhancer | 11 | 13292864 | A | G | 0.57 | IBS | 0.94 (0.92–0.96) | 1.8E-07 | |
| rs2279284 | Promoter | 11 | 13298750 | T | C | 0.27 | IBS | 1.06 (1.04–1.08) | 5.3E-07 | |
| rs2279285 | Promoter | 11 | 13298687 | T | G | 0.70 | IBS | 0.94 (0.92–0.96) | 9.4E-08 | |
| rs2279286 | Promoter | 11 | 13298519 | A | G | 0.70 | IBS | 0.94 (0.92–0.96) | 8.4E-08 | |
| rs2279287 | Promoter | 11 | 13298485 | T | C | 0.30 | IBS | 1.06 (1.04–1.08) | 8.4E-08 | |
| rs2403661 | Enhancer | 11 | 13285281 | T | G | 0.30 | IBS | 1.07 (1.05–1.09) | 3.6E-08 | |
| rs34148132 | Enhancer | 11 | 13314475 | T | C | 0.29 | IBS | 1.06 (1.04–1.08) | 8.2E-08 | |
| rs34796300 | Enhancer | 11 | 13315205 | T | C | 0.43 | IBS | 1.06 (1.04–1.08) | 2.9E-07 | |
| rs4603287 | Promoter | 11 | 13301335 | T | G | 0.29 | IBS | 1.06 (1.04–1.08) | 1.5E-07 | |
| rs4757138 | Promoter | 11 | 13297925 | A | G | 0.30 | IBS | 1.06 (1.04–1.08) | 8.8E-08 | |
| rs4757139 | Promoter | 11 | 13300456 | T | C | 0.70 | IBS | 0.94 (0.92–0.96) | 1.3E-07 | |
| rs4757140 | Promoter | 11 | 13300540 | T | G | 0.70 | IBS | 0.94 (0.92–0.96) | 1.4E-07 | |
| rs55769038 | Enhancer | 11 | 13331808 | A | G | 0.59 | IBS | 0.94 (0.92–0.96) | 6.1E-07 | |
| rs61882122 | Promoter | 11 | 13299895 | A | G | 0.30 | IBS | 1.06 (1.04–1.08) | 9.7E-08 | |
| rs6486116 | CTCF binding site | 11 | 13319838 | A | C | 0.29 | IBS | 1.06 (1.04–1.08) | 6.3E-07 | |
| rs6486118 | Enhancer | 11 | 13323786 | A | G | 0.71 | IBS | 0.94 (0.92–0.96) | 4.0E-07 | |
| rs6486119 | Enhancer | 11 | 13323789 | T | C | 0.29 | IBS | 1.06 (1.04–1.08) | 4.3E-07 | |
| rs6486120 | Enhancer | 11 | 13324142 | T | G | 0.29 | IBS | 1.06 (1.04–1.08) | 5.1E-07 | |
| rs7114573 | Enhancer | 11 | 13323498 | A | C | 0.29 | IBS | 1.06 (1.04–1.08) | 5.2E-07 | |
| rs7125487 | Enhancer | 11 | 13282058 | C | G | 0.28 | IBS | 1.07 (1.05–1.09) | 1.3E-07 | |
| rs72867447 | Promoter | 11 | 13301875 | C | G | 0.43 | IBS | 1.06 (1.04–1.08) | 3.3E-07 | |
| rs7928655 | Promoter | 11 | 13300252 | C | G | 0.30 | IBS | 1.06 (1.04–1.08) | 8.7E-08 | |
| rs7937432 | CTCF binding site | 11 | 13320525 | A | G | 0.71 | IBS | 0.94 (0.92–0.96) | 4.1E-07 | |
| rs7938307 | CTCF binding site | 11 | 13320526 | A | C | 0.71 | IBS | 0.94 (0.92–0.96) | 3.7E-07 | |
| rs7949336 | CTCF binding site | 11 | 13319894 | A | G | 0.74 | IBS | 0.94 (0.92–0.96) | 7.6E-07 | |
| rs7951393 | Enhancer | 11 | 13318431 | T | C | 0.71 | IBS | 0.94 (0.92–0.96) | 4.7E-07 | |
| rs998089 | Enhancer | 11 | 13284111 | T | C | 0.27 | IBS | 1.06 (1.04–1.08) | 4.5E-07 | |
|
rs9517497 DOCK9 |
rs6491472 | Enhancer | 13 | 99598367 | A | G | 0.37 | IBS | 0.94 (0.92–0.96) | 3.1E-08 |
| rs7337807 | Enhancer | 13 | 99610581 | A | C | 0.63 | IBS | 1.06 (1.04–1.08) | 3.8E-08 | |
| rs7338982 | Enhancer | 13 | 99610373 | T | C | 0.63 | IBS | 1.06 (1.04–1.08) | 3.6E-08 | |
| rs7339076 | Enhancer | 13 | 99599128 | C | G | 0.63 | IBS | 1.06 (1.04–1.08) | 4.1E-08 | |
| rs7987680 | Enhancer | 13 | 99601519 | T | G | 0.63 | IBS | 1.06 (1.04–1.08) | 4.7E-08 | |
| rs9513513 | Open chromatin region | 13 | 99595622 | T | C | 0.63 | IBS | 1.06 (1.04–1.08) | 2.4E-08 | |
| rs9517497 | Open chromatin region | 13 | 99594953 | T | C | 0.63 | IBS | 1.07 (1.04–1.09) | 2.3E-08 | |
| rs9517502 | Enhancer | 13 | 99599727 | A | C | 0.37 | IBS | 0.94 (0.92–0.96) | 4.5E-08 | |
| rs9517503 | Enhancer | 13 | 99600658 | A | G | 0.63 | IBS | 1.06 (1.04–1.08) | 4.6E-08 | |
| rs9517508 | Enhancer | 13 | 99606192 | T | G | 0.37 | IBS | 0.94 (0.92–0.96) | 5.2E-08 | |
| rs9557097 | Enhancer | 13 | 99612588 | T | C | 0.62 | IBS | 1.06 (1.04–1.08) | 9.4E-08 | |
NOTE. Functional consequence of variants was performed using the Ensembl Variant Effect Predictor tool (https://grch37.ensembl.org/info/docs/tools/vep). OR: mean effects described to the risk allele in the meta-analysis.
BP, base-pair position (genome build hg19); CHR, chromosome; CI, confidence interval; EA, effect allele; EAF, effect allele frequency; GWAS, genome-wide association study; IBS, irritable bowel syndrome; IBS-M, irritable bowel syndrome mixed subtype; LL, Lifelines; OA, other allele; OR, odds ratio; SNP, single-nucleotide polymorphism; UKBB, UK Biobank.