Table 1. Top 30 filtered SNP-miR-probe associations, sorted based on their context+ scores.
| MRE-SNP | Effect a | Alleles | MAF b | No. of eQTL proxies c | Illumina probe | MeanZ-Score d | Gene | miRNA | Context+ score | miRSVR | miRanda score | Type e |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs10187 | D | C/T | 0.06 | 1 | ILMN_2409062 | 13.39 | ISCU | miR-210-3p | -0.55 | -1.10 | 154 | C |
| rs11932 | D | C/T | 0.17 | 16 | ILMN_1676005 | 5.69 | KPNA1 | miR-210-3p | -0.47 | -0.22 | 152 | U |
| rs7676 | C | T/C | 0.19 | 6 | ILMN_1682812 | 7.17 | C21orf33 | miR-423-5p | -0.45 | -0.72 | 145 | C |
| ILMN_1737588 | 7.01 | C | ||||||||||
| ILMN_2386205 | 10.11 | C | ||||||||||
| rs4476230 | C | T/G | 0.47 | 1 | ILMN_1733937 | 8.92 | MMD | miR-210-3p | -0.42 | n.a. | 147 | C |
| rs2781667 | D | C/T | 0.28 | 6 | ILMN_1674506 | 4.79 | MED23 | miR-361-3p | -0.35 | -0.92 | 152 | U |
| rs4245739 | C | A/C | 0.32 | 1 | ILMN_1746020 | 18.27 | MDM4 | miR-191-5p | -0.32 | -0.61 | 155 | C |
| rs2255015 | C | G/A | 0.48 | 1 | ILMN_1688464 | 23.48 | MAP6D1 | miR-148a-3p | -0.32 | n.a. | 144 | C |
| miR-148b-3p | -0.32 | n.a. | 150 | C | ||||||||
| rs444271 | C | G/C | 0.12 | 1 | ILMN_2345142 | 6.56 | SULF2 | miR-140-3p | -0.31 | -0.23 | 145 | U |
| rs1136808 | D | G/C | 0.41 | 16 | ILMN_1743032 | 26.67 | CTSS | miR-423-5p | -0.31 | -0.13 | 146 | C |
| rs10039796 | C | C/G | 0.48 | 1 | ILMN_1658962 | 4.29 | LCP2 | miR-365a-3p | -0.29 | -0.84 | 162 | U |
| rs17765088 | D | C/G | 0.13 | 1 | ILMN_2337386 | 4.79 | CCR9 | miR-335-5p | -0.29 | -0.33 | 153 | U |
| rs6728 | D | C/G | 0.26 | 4 | ILMN_1694084 | 12.54 | CYTH1 | miR-10a-5p | -0.29 | -0.97 | 153 | U |
| ILMN_2403852 | 5.66 | U | ||||||||||
| rs3828609 | D | T/C | 0.15 | 3 | ILMN_1686623 | 17.91 | CSF1R | miR-155-5p | -0.28 | -1.01 | 148 | U |
| rs12190214 | D | C/A | 0.13 | 1 | ILMN_2372398 | 5.65 | ALDH5A1 | miR-210-3p | -0.28 | -0.80 | 140 | C |
| rs11730 | D | A/G | 0.47 | 7 | ILMN_1739541 | 25.69 | NMI | miR-148a-3p | -0.28 | -1.18 | 154 | C |
| miR-148b-3p | -0.28 | -1.18 | 146 | C | ||||||||
| rs1135314 | C | A/G | 0.43 | 1 | ILMN_1712532 | 26.69 | CARD9 | miR-148a-3p | -0.27 | n.a. | 145 | U |
| miR-148b-3p | -0.27 | n.a. | 146 | U | ||||||||
| rs1057560 | C | A/G | 0.50 | 1 | ILMN_1732489 | 14.49 | SLC10A7 | miR-25-3p | -0.26 | -0.31 | 140 | C |
| rs73215937 | C | T/C | 0.17 | 21 | ILMN_1758323 | 20.64 | ACPP | miR-486-3p | -0.26 | n.a. | 150 | C |
| rs13936 | D | G/A | 0.07 | 1 | ILMN_1789909 | 4.07 | TBC1D9B | miR-296-5p | -0.26 | -0.12 | 140 | C |
| rs2287067 | C | T/C | 0.17 | 1 | ILMN_1699275 | 4.13 | VWDE | miR-590-5p | -0.26 | n.a. | 155 | C |
| rs2239680 | D | T/C | 0.26 | 3 | ILMN_2349459 | 8.62 | BIRC5 | miR-335-5p | -0.26 | -0.63 | 157 | U |
| rs10438593 | C | C/T | 0.12 | 1 | ILMN_1699607 | 8.77 | MMP25 | miR-181d-5p | -0.25 | n.a. | 165 | U |
| ILMN_1717207 | 6.40 | U | ||||||||||
| rs1057560 | C | A/G | 0.50 | 1 | ILMN_1732489 | 14.49 | SLC10A7 | miR-92a-3p | -0.25 | -0.31 | 140 | C |
SNPs shown in bold are in experimentally validated MREs.
a SNP effect on miRNA binding: D disrupts an MRE and C creates an MRE.
b MAF is based on 1000G pilot 1 CEU population.
c Number of cis-eQTL SNPs from the LD block (R2 = 1, 1000G pilot 1, CEU)
d Z-scores from a recent meta-analysis [21] are averaged for LD block (R2 = 1); FDR < 0.05 for all associations.
e Association type: C-concordant; U-unconcordant.