Table 2. Associations between miRNA expression and SNPs in miRNA genes and miRNA-target genes by genotype in non-tumor tissue (adjusted for age, sex and center).
| AA | AB | BB | p-values | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Gene(s) | SNP | miRNA | N | Mean | % 0 Exp | N | Mean | % 0 Exp | N | Mean | % 0 Exp | Raw | FDR | Variant Type 3 |
| miRNA | ||||||||||||||
| CD22, MIR5196 | rs10406069, 0 = GG 1 = GA 2 = AA | hsa-miR-5196-5p | 218 | 64.14 | 0.00 | 105 | 60.93 | 0.00 | 21 | 61.38 | 0.00 | 0.029 | 0.52 | IN, DS, MS, 3' UTR, of CD22. NC, NCE of MIR5196. |
| MCM7, MIR106B, MIR25, MIR93 | rs1527423, 0 = AA 1 = AG 2 = GG | hsa-miR-25-3p | 86 | 14.51 | 9.30 | 182 | 12.40 | 10.44 | 76 | 10.41 | 21.05 | 0.004 | 0.49 | DS of COPS6. IN, NC, DS, NMD of MCM7. UP of MIR106B, MIR25, MIR93. |
| GNN, HSP90B1, MIR3652 | rs17797090, 0 = GG 1 = GA 2 = AA | hsa-miR-3652 | 288 | 159.68 | 0.00 | 56 | 145.86 | 0.00 | 0 | NA | NA | 0.032 | 0.52 | RR. TFB, 5' UTR, NMD, NC, NCE, IN of HSP90B1. NCE, NC of MIR3652. UP of RP11-642P15. |
| MIR146A | rs2910164, 0 = GG 1 = GC 2 = CC | hsa-miR-146a-5p | 197 | 8.24 | 32.49 | 129 | 8.29 | 31.01 | 18 | 6.61 | 5.56 | 0.038 | 0.52 | NC, NCE. |
| MIR1307, USMG5 | rs7911488, 0 = AA 1 = AG 2 = GG | hsa-miR-1307-3p | 154 | 13.03 | 0.00 | 153 | 13.03 | 0.65 | 37 | 11.27 | 0.00 | 0.019 | 0.52 | NC, NCE of MIR1307. UP of PDCD11. IN, 5' UTR of USMG5. |
| RPL17, RPL17-C18orf32, SNORD58A, SNORD58 | rs1943676, 0 = AA 1 = AG 2 = GG | hsa-miR-1539 | 147 | 4.24 | 36.73 | 167 | 4.10 | 53.89 | 30 | 4.02 | 56.67 | 0.004 | 0.49 | RR. UP of C18orf32. IN, NC, DS of MIR1539. SP, IN, NC, NCE, UP of RPL17. UP, DS of SNORD58A, SNORD58B, SNORD58C. DS of SRP72P1. |
| miRNA-Target | ||||||||||||||
| NRSN1 | rs1053047, 0 = GG 1 = GA 2 = AA | hsa-miR-143-5p | 92 | 3.96 | 94.57 | 175 | 3.39 | 92.57 | 77 | 5.36 | 84.42 | 0.029 | 0.52 | 3' UTR, DS, IN. |
| KIAA0423 (FAM179B)* | rs1053667, 0 = TT 1 = TC 2 = CC | hsa-miR-19b-3p | 305 | 11.19 | 14.10 | 39 | 13.44 | 28.21 | 0 | NA | NA | 0.028 | 0.52 | DS, 3' UTR, NMD. |
| SLC10A7 | rs1057560, 0 = GG 1 = GA 2 = AA | hsa-miR-25-3p | 97 | 11.54 | 14.43 | 171 | 12.39 | 13.45 | 76 | 14.09 | 7.89 | 0.039 | 0.52 | RR. 3' UTR, DS. |
| DNM2 | rs12232826, 0 = GG 1 = GT 2 = TT | hsa-miR-638 | 314 | 3980.05 | 0.00 | 30 | 4412.26 | 0.00 | 0 | NA | NA | 0.013 | 0.52 | IN. |
| CSK | rs1378940, 0 = AA 1 = AC 2 = CC | hsa-miR-4513 | 159 | 27.91 | 0.00 | 139 | 30.08 | 0.00 | 46 | 30.68 | 0.00 | 0.027 | 0.52 | RR. UP, IN, NC. |
| hsa-miR-1207-5p | 212 | 2043.96 | 0.00 | 117 | 1911.72 | 0.00 | 15 | 1699.90 | 0.00 | 0.016 | 0.52 | |||
| ICOS | rs1559931, 0 = GG 1 = GA 2 = AA | hsa-miR-196b-5p | 212 | 9.00 | 24.53 | 117 | 8.24 | 16.24 | 15 | 6.35 | 0.00 | 0.037 | 0.52 | RR. 3' UTR. |
| hsa-miR-2117 | 212 | 4.53 | 50.47 | 117 | 4.61 | 46.15 | 15 | 4.74 | 20.00 | 0.033 | 0.52 | |||
| LAD1 | rs16848494, 0 = CC 1 = CT 2 = TT | hsa-miR-143-5p | 328 | 4.28 | 90.85 | 16 | 0.00 | 100.00 | 0 | NA | NA | 0.027 | 0.52 | DS, 3' UTR, IN of LAD1. UP of TNNT2. |
| AFF1 | rs17703261, 0 = AA 1 = AT 2 = TT | hsa-miR-648 | 211 | 18.23 | 0.00 | 121 | 17.48 | 0.00 | 12 | 14.98 | 0.00 | 0.022 | 0.52 | 3' UTR, DS. |
| hsa-miR-1207-5p | 212 | 2043.96 | 0.00 | 117 | 1911.72 | 0.00 | 15 | 1699.90 | 0.00 | 0.020 | 0.52 | |||
| ICOS | rs4404254, 0 = TT 1 = TC 2 = CC | hsa-miR-196b-5p | 212 | 9.00 | 24.53 | 117 | 8.24 | 16.24 | 15 | 6.35 | 0.00 | 0.034 | 0.52 | 3' UTR. |
| hsa-miR-2117 | 212 | 4.53 | 50.47 | 117 | 4.61 | 46.15 | 15 | 4.74 | 20.00 | 0.035 | 0.52 | |||
| NKAIN4, FLJ16779 | rs720607, 0 = GG 1 = GA 2 = AA | hsa-miR-3196 | 112 | 1415.24 | 0.00 | 163 | 1326.52 | 0.00 | 69 | 1269.88 | 0.00 | 0.027 | 0.52 | RR. IN. |
| CD80 | rs7628626, 0 = CC 1 = CA 2 = AA | hsa-miR-2117 | 233 | 4.67 | 42.06 | 98 | 4.40 | 62.24 | 13 | 3.69 | 38.46 | 0.010 | 0.52 | RR. DS, 3' UTR, of CD80. DS of TIMMDC1. |
| FGF2 | rs7683093, 0 = CC 1 = CG 2 = GG | hsa-miR-92b-3p | 249 | 1.34 | 93.17 | 84 | 2.01 | 82.14 | 11 | 0.73 | 81.82 | 0.008 | 0.52 | RR. DS, 3' UTR of FGF2. IN, NMD, DS, US of NUDT6. |
| BRCA1 | rs8176318, 0 = CC 1 = CA 2 = AA | hsa-miR-525-5p | 165 | 3.20 | 46.67 | 130 | 3.16 | 51.54 | 49 | 3.85 | 69.39 | 0.035 | 0.52 | 3' UTR, DS. |
| PARP1 | rs8679, 0 = AA 1 = AG 2 = GG | hsa-miR-630 | 212 | 364.38 | 0.00 | 106 | 392.44 | 0.00 | 26 | 541.85 | 0.00 | 0.013 | 0.52 | 3' UTR, DS. |
| SELS (VIMP)* | rs9874, 0 = TT 1 = TC 2 = CC | hsa-miR-181a-5p | 268 | 25.24 | 0.00 | 69 | 29.71 | 0.00 | 7 | 25.02 | 0.00 | 0.027 | 0.52 | 3' UTR, DS. |
| MCM7, AP4M1 | rs999885, 0 = AA 1 = AG 2 = GG | hsa-miR-25-3p | 88 | 14.45 | 9.09 | 180 | 12.36 | 10.00 | 76 | 10.51 | 22.37 | 0.003 | 0.49 | IN, NMD, UP, NC, DS of AP4M1. UP of MCM7. DS of TAF6. |
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.
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.
*Names in parentheses are alternatives.