Table 1.
Sentinel cis-exQTL variants and their associated ex-miRNAs
| miRNA | Sentinel SNP | Chr | SNP Position (hg38) | Effect Allele | Other Allele | EAF | FHS |
RS |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Betaa | SE | p value | Betaa | SE | p value | |||||||
| miR-1290 | rs7524223 | 1 | 18906196 | G | A | 0.009 | −1.44 | 0.26 | 4.3E-08 | – | – | – |
| miR-9-3p | rs139213408 | 1 | 156878571 | C | T | 0.005 | −3.63 | 0.62 | 6.0E-09 | – | – | – |
| miR-181a-5p | rs10919655 | 1 | 199279533 | G | A | 0.339 | −0.33 | 0.05 | 6.5E-11 | 0.11 | 0.013 | 5.2E-16 |
| miR-181b-5p | rs138900185 | 1 | 198702776 | A | G | 0.006 | −1.78 | 0.29 | 6.7E-10 | – | – | – |
| miR-562 | rs766631473 | 2 | 232828371 | C | CT | 0.005 | −15.01 | 2.11 | 2.3E-12 | – | – | – |
| miR-582-5p | rs5024245 | 5 | 60250066 | A | G | 0.481 | −0.42 | 0.06 | 1.0E-12 | – | – | – |
| miR-584-5p | rs36047 | 5 | 149061758 | T | C | 0.355 | −0.32 | 0.05 | 1.7E-10 | 0.23 | 0.026 | 6.9E-19 |
| miR-605-5p | rs60202580 | 10 | 51908729 | C | A | 0.009 | −13.82 | 1.98 | 1.5E-11 | – | – | – |
| miR-130a-3p | rs7117896 | 11 | 57621078 | A | G | 0.277 | −0.32 | 0.06 | 2.8E-08 | 0.30 | 0.023 | 7.1E-39 |
| miR-16-1-3p | rs116939667 | 13 | 49344847 | T | A | 0.006 | −2.58 | 0.47 | 3.6E-08 | – | – | – |
| miR-4306 | rs140415911 | 13 | 99168139 | C | T | 0.013 | 1.22 | 0.22 | 4.7E-08 | – | – | – |
| miR-625-3p (14q23)b | rs2127870 | 14 | 65330128 | C | G | 0.748 | 1.01 | 0.06 | 2.2E-59 | 0.36 | 0.022 | 3.9E-60 |
| miR-369-5p (14q32) | rs7144855 | 14 | 100400292 | C | G | 0.004 | −6.80 | 0.86 | 3.0E-15 | – | – | – |
| miR-136-5p (14q32) | rs11622192 | 14 | 100549853 | A | G | 0.221 | 0.58 | 0.10 | 6.4E-9 | – | – | – |
| miR-127-3p, miR-134-5p, miR-136-3p, miR-154-5p, miR-369-3p, miR-376a-3p, miR-376c-3p, miR-382-5p, miR-431-5p, miR-433-3p, miR-485-3p, miR-494-3p, miR-495-3p, miR-543, miR-656-3p (14q32) | rs12881545 (rs12881760 or rs72700576, r2 = 1) | 14 | 100709875 | C | G | 0.643 | −0.56 | 0.05 | 3.5E-24 | 0.25 | 0.028 | 1.8E-19 |
| miR-629-5p | rs78212770 | 15 | 70079438 | G | C | 0.019 | 1.06 | 0.18 | 7.1E-09 | – | – | – |
| miR-125a-3p | rs1181776908 | 19 | 51311263 | G | A | 0.003 | −5.38 | 0.96 | 2.4E-08 | – | – | – |
| miR-373-3p | rs145507432 | 19 | 53293768 | C | T | 0.013 | −7.73 | 1.17 | 1.4E-10 | – | – | – |
| miR-1323 | rs562999849 | 19 | 54390570 | A | AC | 0.006 | −11.05 | 1.98 | 3.9E-08 | – | – | – |
| miR-499a-3p | rs1433162886 | 20 | 35110006 | C | A | 0.004 | −15.17 | 2.48 | 1.9E-09 | – | – | – |
| miR-499a-5p | rs1343050945 | 20 | 34837329 | A | C | 0.004 | −2.24 | 0.38 | 4.5E-09 | – | – | – |
| miR-133a-3p, miR-1-3p | rs12624608 | 20 | 62558091 | A | C | 0.242 | −0.67 | 0.07 | 1.41E-22 | 0.17 | 0.025 | 4.3E-12 |
EAF: effect allele frequency; Beta: effect beta value; SE: standard error.
Please note that in FHS, expression levels of ex-miRNAs were quantified using Ct values. It’s essential to grasp that in this context, a higher Ct value signifies a lower expression level of the miRNA. Thus, when interpreting the results presented in this table, a positive beta value indicates that the effect allele increased miRNA Ct values (resulting in decreased expression), and vice versa. Conversely, in RS, expression levels of ex-miRNAs were reported using conventional values derived from miRNA-seq, where higher values indicate higher expression levels. Consequently, positive beta values in RS signify that the effect allele increased miRNA expression.
In RS, expression levels of miR-625-5p were measured instead of miR-625-3p. It’s noteworthy that the effect direction of cis-exQTLs with miR-625-5p in RS is opposite to that observed with miR-625-3p in FHS.