Table 3. Associations of miRNA expression by SNPs in miRNA genes and miRNA-target genes between tumor and non-tumor tissues (adjusted for age, sex, and center).
| AA | AB | BB | p-values | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene(s) | SNP | miRNA | N | Mean | T % 0 Exp | N % 0 Exp | N | Mean | T % 0 Exp | N % 0 Exp | N | Mean | T % 0 Exp | N % 0 Exp | Raw | FDR | Variant Type 3 |
| miRNA | |||||||||||||||||
| MIR605, PRKG1 | rs2043556, 0 = TT 1 = TC 2 = CC | hsa-miR-605 | 259 | -1.07 | 79.92 | 51.35 | 110 | -0.36 | 75.45 | 61.82 | 14 | 0.53 | 64.29 | 57.14 | 0.007 | 0.36 | RR. NC, NCE of MIR605. IN of PRKG1. US of RP11-539E19.2. |
| MIR548AP | rs2344843, 0 = AA 1 = AG 2 = GG | hsa-miR-548ap-5p | 163 | 0.39 | 96.93 | 88.96 | 167 | -0.42 | 98.80 | 85.03 | 53 | -0.66 | 100.00 | 84.91 | 0.029 | 0.54 | DS of MIR548AP. |
| MIR146A | rs2910164, 0 = GG 1 = GC 2 = CC | hsa-miR-146a-5p | 218 | 3.62 | 26.61 | 27.52 | 146 | -0.21 | 43.15 | 26.71 | 19 | 2.96 | 31.58 | 5.26 | 0.002 | 0.30 | NC, NCE. |
| MIR143 | rs353292, 0 = GG 1 = GA 2 = AA | hsa-miR-143-5p | 105 | 4.46 | 88.57 | 96.19 | 204 | -0.28 | 91.18 | 87.25 | 74 | -0.22 | 94.59 | 87.84 | 0.019 | 0.54 | US of MIR143. DS, NC, NCE of |
| hsa-miR-145-3p | 105 | 2.95 | 95.24 | 98.10 | 204 | -0.44 | 96.57 | 93.14 | 74 | -2.22 | 100.00 | 91.89 | 0.008 | 0.36 | MIR143HG. UP of MIR145. | ||
| MIR182 | rs76481776 (related SNP) 1 | hsa-miR-182-5p | 311 | 2.16 | 88.10 | 100.00 | 72 | 3.22 | 97.22 | 100.00 | 0 | NA | NA | NA | 0.024 | 0.54 | INTERGENIC VARIANT. |
| rs2693737, 0 = AA 1 = AG 2 = GG | |||||||||||||||||
| MIR143 | rs353293, 0 = CC 1 = CT 2 = TT | hsa-miR-143-5p | 106 | 4.46 | 88.68 | 96.23 | 203 | -0.28 | 91.13 | 87.19 | 74 | -0.22 | 94.59 | 87.84 | 0.014 | 0.47 | US of MIR143. DS, NC, NCE, IN of |
| hsa-miR-145-3p | 106 | 2.95 | 95.28 | 98.11 | 203 | -0.44 | 96.55 | 93.10 | 74 | -2.22 | 100.00 | 91.89 | 0.008 | 0.36 | MIR143HG. UP of MIR145. | ||
| miRNA-Target | |||||||||||||||||
| CAMK1D | rs10508445, 0 = AA 1 = AG 2 = GG | hsa-miR-4481 | 112 | -9.41 | 0.00 | 0.00 | 193 | -4.02 | 0.00 | 0.00 | 78 | 0.84 | 0.00 | 0.00 | 0.022 | 0.54 | IN, NC. |
| SLC10A7 | rs1057560, 0 = GG 1 = GA 2 = AA | hsa-miR-25-3p | 104 | 13.75 | 3.85 | 13.46 | 189 | 14.00 | 4.23 | 11.11 | 90 | 12.33 | 10.00 | 6.67 | 0.007 | 0.36 | RR. 3' UTR, DS. |
| GRINL1A | rs1062707, 0 = TT 1 = TC 2 = CC | hsa-miR-424-3p | 226 | 13.46 | 0.00 | 0.44 | 131 | 9.62 | 0.00 | 0.00 | 26 | 7.90 | 0.00 | 0.00 | 0.025 | 0.54 | IN, NC, DS, MND, 3' UTR, SN of GCOM1 7 . 3' UTR, NMD, SN, IN, |
| hsa-miR-424-5p | 226 | 4.37 | 66.37 | 89.82 | 131 | 2.65 | 68.70 | 87.02 | 26 | -0.05 | 76.92 | 88.46 | 0.022 | 0.54 | NC, NCE of POLR2M7. | ||
| KSR2 | rs11068503, 0 = TT 1 = TC 2 = CC | hsa-miR-149-3p | 126 | 1.33 | 0.00 | 0.00 | 178 | -1.79 | 0.00 | 0.00 | 79 | -4.84 | 0.00 | 0.00 | 0.007 | 0.36 | 3' UTR, DS. |
| EGFL7, LOC101928-612 | rs1332793, 0 = TT 1 = TC 2 = CC | hsa-miR-126-3p | 151 | 0.87 | 6.62 | 9.27 | 183 | -1.63 | 10.93 | 5.46 | 49 | 0.07 | 10.20 | 4.08 | 0.011 | 0.39 | US, IN of EGFL7. US of RP11-251M1.1. |
| VTCN1 | rs13505, 0 = AA 1 = AC 2 = CC | hsa-miR-196a-5p | 207 | 1.66 | 42.03 | 25.12 | 147 | 2.52 | 40.82 | 27.89 | 29 | 3.51 | 17.24 | 27.59 | 0.036 | 0.64 | RR. 3' UTR, DS. |
| CD86 | rs17281995, 0 = GG 1 = GC 2 = CC | hsa-miR-212-3p | 274 | 0.35 | 3.65 | 4.74 | 100 | -0.53 | 9.00 | 8.00 | 9 | -2.73 | 22.22 | 0.00 | 0.047 | 0.73 | 3’ UTR, DS. |
| IL6ST | rs2228043, 0 = GG 1 = GC 2 = CC | hsa-miR-221-3p | 298 | 8.21 | 15.10 | 35.57 | 85 | 11.62 | 12.94 | 45.88 | 0 | NA | NA | NA | 0.027 | 0.54 | 3' UTR, US, NC, NCE, MS, NMD, IN. |
| WWP2 | rs2270841, 0 = CC 1 = CT 2 = TT | hsa-miR-140-3p | 199 | -3.36 | 24.12 | 12.56 | 154 | -1.51 | 18.83 | 11.69 | 30 | -0.79 | 16.67 | 13.33 | 0.025 | 0.54 | DS of MIR140. SN, US, NC, NCE, DS of WWP2. |
| TAF1C | rs2288024, 0 = TT 1 = TC 2 = CC | hsa-miR-103a-3p | 358 | 14.46 | 3.07 | 0.84 | 25 | 22.63 | 0.00 | 0.00 | 0 | NA | NA | NA | 0.009 | 0.39 | 3' UTR, DS, IN, NC, NCE of DNAAF1. DS, 3' UTR, NC, NCE of TAF1C. |
| TNFRSF4 | rs2298209, 0 = GG 1 = GC 2 = CC | hsa-miR-200b-3p | 374 | 14.66 | 2.14 | 0.27 | 9 | 57.69 | 0.00 | 0.00 | 0 | NA | NA | NA | 0.043 | 0.70 | DS, NC, NCE, 3’ UTR of TNFRSF4. UP of TNFRSF18. |
| IL22RA2 | rs276466, 0 = AA 1 = AG 2 = GG | hsa-miR-30c-2-3p | 212 | 0.47 | 9.43 | 13.21 | 149 | -0.31 | 11.41 | 8.72 | 22 | -1.07 | 22.73 | 4.55 | 0.001 | 0.22 | 3' UTR. |
| ZNF396 | rs2909339, 0 = GG 1 = GA 2 = AA | hsa-miR-145-3p | 267 | -0.67 | 97.75 | 93.26 | 105 | 1.84 | 94.29 | 97.14 | 11 | -0.22 | 100.00 | 90.91 | 0.038 | 0.64 | DS, 3' UTR. |
| PRKAR1A | rs8905, 0 = TT 1 = TG 2 = GG | hsa-miR-214-3p | 285 | 5.60 | 15.79 | 13.33 | 87 | 6.97 | 6.90 | 17.24 | 11 | 9.22 | 9.09 | 27.27 | 0.006 | 0.36 | DS of FAM20. 3' UTR, DS, IN, NMD of PRKR1A. |
| ZNF257 | rs9304994, 0 = AA 1 = AG 2 = GG | hsa-miR-557 | 135 | 8.03 | 0.00 | 0.00 | 183 | -0.62 | 0.00 | 0.00 | 65 | -2.80 | 0.00 | 0.00 | 0.029 | 0.54 | 3' UTR, NMD, DS. |
1Related SNPs are those in linkage disequilibrium to SNPs within the dataset.
2EX: Exon; DS: Downstream; IN: intron; MS: Missense; NC: Non-coding; NCE: Non-coding exon; NMD: Nonsense-mediated decay; RR: Regulatory region; SN: Synonymous; SPR: Splice Region; TFB: Transcription Factor Binding site; US: Upstream.
3Variant Analysis was performed with Ensembl's VEP (GRCh37.p13). Multiple type of variants are listed for a given gene when these variant occur in different transcripts. Some additional genes not analyzed are listed by VEP.
4This SNP has now merged into a new SNP (GRCh38).
5For miRNA Gene Regions this column has the miRNA with the SNP; for miRNA-target genes this column has the associated miRNA for the mRNA with the SNP.
6Association seen in literature.
7Related genes/proteins of gene analyzed.