Table 2.
SNPs that are missense mutations from the 1000 Genome Project and that are in LD (r2>=0.9) with primary signals from the known and newly identified loci that achieve genomewide significance in the meta-analysis, or with secondary signals from the conditional analysis (“Index SNP”). The “Index SNP” columns show the information of SNPs with the most significant P-value in our analysis, and the “Potential causal SNP” columns show the information for the SNPs that have high LD with our strongest signal. The “Combined p-value” column shows the meta-analysis P-value for the index SNP, potential causal SNP, and the P-values for the index SNPs while conditioning on the potential causal SNPs, respectively. Note the potential causal SNP rs7199949 is not present in our meta-analysis study therefore its P-value is not shown.
| Index SNP
|
Potential Causal SNP
|
Combined P-value
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Markera | RAF | Annotation | Markerc | RAF | Gene with variant | Amino acid substitution (Damaging effectd) | r2 | Index SNP | Potential causal SNP | Index SNP (conditioning on causal SNP) |
| rs9988642 | 0.93 | 454bp downstream IL23R | rs11209026 | 0.94 | IL23R | R381Q (P) | 0.91 | 1.1×10−26 | 1.5×10−26 | 0.13 |
| rs27432 | 0.29 | Intron ERAP1 | rs27044 | 0.29 | ERAP1 | Q730E | 1 | 1.9×10−20 | 2.3×10−20 | 0.14 |
| rs1295685 | 0.77 | 3′ UTR IL13 | rs20541 | 0.77 | IL13 | R144Q | 0.97 | 3.4×10−10 | 3.5×10−10 | 0.78 |
| rs33980500 | 0.09 | Missense | Self | 0.09 | TRAF3IP2 | D19N (S/P) | 1 | 4.2×10−45 | 4.2×10−45 | NA |
| rs2066819 | 0.93 | Intron STAT2 | rs2066807 | 0.93 | STAT2 | M594I | 0.9 | 5.4×10−17 | 5.1×10−16 | 0.036 |
| rs12445568 | 0.36 | Intron STX1B | rs7199949 | 0.37 | PRSS53 | P406A | 0.9 | 1.2×10−16 | NA | NA |
| rs11652075 | 0.51 | Missense | Self | 0.51 | CARD14 | R820W (S) | 1 | 3.4×10−8 | 3.4×10−8 | NA |
| rs34536443 | 0.97 | Missense | Self | 0.97 | TYK2 | P1104A (S/P) | 1 | 1.5×10−39 | 1.5×10−39 | NA |
| rs12720356b | 0.9 | Missense | Self | 0.9 | TYK2 | I684S (S/P) | 1 | 3.2×10−10 | 3.2×10−10 | NA |
| rs4821124 | 0.19 | 966bp downstream UBE2L3 | rs2298428 | 0.18 | YDJC | A263T | 0.96 | 3.8×10−8 | 6.2×10−8 | 0.48 |
SNPs with the most significant p-value in our analysis.
The meta-analysis p-value from the conditional analysis is shown.
SNPs that are missense mutations and have high LD with our strongest signal.
High confidence damaging effect predicted by SIFT (S) or Polyphen (P). RAF: Risk Allele Frequency. For the potential causal SNP rs7199949, the P value is ‘NA’ as the SNP was not included on the Immunochip.