Table 2.
Top novel associations for IBD, CD and UC
| Phenotype | Leading SNP | Chr | Position | Annotation | A1 | A2 | Gene | log10BF | PPAHet |
Total
sample size |
Direction |
Effect
allele Freq. AA |
Effect
allele Freq. EUR |
Effect
allele Freq. EAS |
PMAE-AA | PMAE-EUR | PMAE-EAS |
Number of
significant SNPs in locus |
Significant SNPs in
locus |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IBD | rs2986751 | 1 | 6 534 781 | UTR5 | A | G |
PLEKHG5; TNFSFR25 |
6.21 | 0.07 | 41 999 | − | 0.291 | 0.065 | -0.174 | -0.171 | 1 | |||
| IBD | rs3811406 | 1 | 151 254 041 | ncRNA_ Exonic |
A | G |
BC021024; PI4KB; PSMD4 |
8.06 | 0.073 | 100 530 | − | 0.200 | 0.230 | 0.370 | -0.072 | -0.071 | -0.070 | 2 | rs3811406*, rs2031797 |
| IBD | rs12532822 | 7 | 37 393 177 | UTR5 | A | C | ELMO1 | 8.24 | 1 | 100 530 | − + − | 0.053 | 0.171 | 0.048 | -0.011 | 0.049 | -0.473 | 1 | |
| IBD | rs79315643 | 8 | 10 773 414 | Intronic | A | G | XKR6 | 23.38 | 1 | 100 530 | +++ | 0.869 | 0.780 | 0.905 | 0.056 | 0.012 | 0.732 | 1 | |
| IBD | rs230261 | 19 | 36 363 470 | Exonic | A | G | APLP1 | 6.14 | 0.186 | 100 530 | ++− | 0.115 | 0.030 | 0.002 | 0.138 | 0.141 | 0.123 | 1 | |
| CD | rs974801 | 4 | 106 071 064 | Intronic | A | G |
TET2; AK094561 |
7.73 | 0.074 | 74 249 | +++ | 0.707 | 0.620 | 0.385 | 0.069 | 0.069 | 0.068 | 3 | rs17035289, rs974801 rs10010325 |
| CD | rs2293503 | 7 | 70 250 125 | Intronic | T | C | AUTS2 | 6.05 | 1 | 68 840 | +− | 0.463 | 0.439 | 0.187 | -0.090 | 1 | |||
| CD | rs3801944 | 7 | 107 255 548 | Intronic | A | G | BCAP29 | 7.05 | 0.074 | 74 249 | +++ | 0.256 | 0.280 | 0.289 | 0.073 | 0.072 | 0.073 | 3 | rs3801944*, rs10273733, rs2808 |
| CD | rs79315643 | 8 | 10 773 414 | Intronic | A | G | XKR6 | 18.50 | 1 | 74 249 | +++ | 0.869 | 0.780 | 0.905 | 0.123 | 0.010 | 0.811 | 1 | |
| CD | rs230261 | 19 | 36 363 470 | Exonic | A | G | APLP1 | 6.13 | 0.211 | 74 249 | ++− | 0.115 | 0.030 | 0.002 | 0.164 | 0.169 | 0.152 | 1 | |
| CD | rs2143606 | 20 | 42 838 550 | Intronic | A | G | OSER1 | 8.80 | 0.066 | 74 249 | +++ | 0.274 | 0.531 | 0.436 | 0.076 | 0.076 | 0.076 | 1 | |
| UC | rs10465507 | 1 | 173 162 439 | Intronic | A | C | TNFSF4 | 6.18 | 1 | 75 264 | − + − | 0.496 | 0.245 | 0.050 | 0.000 | 0.001 | -0.770 | 1 | |
| UC | rs115484865 | 6 | 29 604 124 | Intergenic | A | G |
GABBR1; MOG |
6.51 | 0.19 | 33 017 | −+ | 0.115 | 0.206 | 0.132 | 0.159 | 1 | |||
| UC | rs16869677 | 6 | 33 876 082 | ncRNA_ Exonic |
A | G | DQ570892 | 11.59 | 1 | 75 264 | + − + | 0.095 | 0.081 | 0.141 | 0.046 | -0.001 | 0.470 | 1 | |
| UC | rs73407795 | 6 | 34 518 271 | Intronic | A | G |
SPDEF; ILRUN |
8.04 | 1 | 75 264 | +++ | 0.141 | 0.064 | 0.061 | 0.053 | 0.051 | 0.526 | 1 | |
| UC | rs3822921 | 6 | 35 057 331 | UTR3 | A | G |
ANKS1A; TCP11; AY927475 |
7.93 | 1 | 75 264 | - − + | 0.024 | 0.127 | 0.058 | -0.038 | -0.030 | 0.539 | 2 | rs3822921*, rs11755266 |
| UC | rs79315643 | 8 | 10 773 414 | Intronic | A | G | XKR6 | 7.23 | 1 | 75 264 | + − + | 0.865 | 0.780 | 0.905 | 0.003 | -0.003 | 0.572 | 1 | |
| UC | rs72661359 | 8 | 79 677 725 | Intronic | A | C | IL7 | 7.88 | 0.993 | 75 264 | −++ | 0.071 | 0.058 | 0.000 | 0.110 | 0.133 | 2.733 | 1 | |
| UC | rs2940716 | 10 | 50 124 724 | Intronic | A | G |
LRRC18; WDFY4 |
7.61 | 1 | 75 264 | −++ | 0.277 | 0.269 | 0.000 | 0.005 | 0.006 | 2.934 | 1 | |
| UC | rs9911533 | 17 | 38 775 476 | Intergenic | A | G |
CCR7; SMARCE1; KRT222; KRT24; KRT25 |
7.98 | 0.099 | 75 264 | +++ | 0.783 | 0.616 | 0.723 | 0.080 | 0.078 | 0.077 | 11 | rs7221109, rs757411, rs9911533*, rs1013971, rs4890093, rs9906785, rs7217237, rs2315020, rs2159430, rs2462963, rs726848 |
Notes: Trans-ancestry association analysis results for all novel SNPs are shown in this table for IBD, CD and UC. The significance threshold for the trans-ancestry meta-analysis was set at log10BF ≥ 6. Summary statistics of GWAS and immunochip data sets were analyzed using MANTRA to identify novel risk loci for each of the three phenotypes. Phenotype, traits of interest (IBD, CD, UC); SNP, single-nucleotide polymorphism; Chr, chromosome; Position, base pair position (hg19); A1, effect allele; A2, other allele; Annotation, the functional classification of the variant; Genes, names of most proximal candidate genes ; log10BF, log 10 Bayes factor in favor of association, PPAHet, posterior probability of association showing evidence of heterogeneity; Total sample size, lists the sample sizes used in the analysis per trait; Effect direction, denotes direction of effect with + for positive allelic effect for effect allele, and − for negative allelic effect for effect allele; Effect Allele Freq., allele frequency of the effect allele for the population; PMAE-AA, posterior mean allelic effect for AA cohort; PMAE-EUR, posterior mean allelic effect for EUR cohort; PMAE-EAS, posterior mean allelic effect for EA cohort; Number of significant SNPs in locus, shows the number of SNPs that met the threshold for significance (log10BF ≥ 6); Significant SNPs in locus, lists the SNPs that met the threshold for significance (log10BF ≥ 6), * denotes the SNP that had the highest Bayes factor in the locus.