Table V.
Class level associations with IL-6 and CRP induced response
| Interleukin 6 (IL-6) | Class-level score test | SNP-level score p-value | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
|
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| Class | Chr | Start♯ | Stop♯ | 𝒞 | t̃‡ | l | δ | p-value | Min | Median | Max | minP rs§ | # SNPs |
| ENSG00000229401.1* | 6 | 10434548 | 10457014 | 38.52 | 47.40 | 11.55 | 0 | 2.81E-06 | 1.00E-04 | 2.62E-04 | 6.60E-01 | rs303064 | 7 |
| EIF3A∘ | 6 | 24544331 | 24646383 | 28.28 | 59.85 | 19.21 | 0 | 4.65E-06 | 3.58E-08 | 2.06E-02 | 9.94E-01 | rs2760166 | 27 |
| RBP3 | 10 | 48381486 | 48390991 | 44.24 | 45.74 | 10.95 | 0 | 3.46E-06 | 3.60E-07 | 6.94E-03 | 2.70E-02 | rs4922515 | 3 |
| EBF3∘,¶ | 10 | 131633495 | 131762091 | 24.69 | 87.78 | 32.18 | 0 | 4.71E-07 | 5.25E-09 | 1.80E-01 | 9.80E-01 | rs4751138 | 26 |
| MED21 | 12 | 27175454 | 27183606 | 48.73 | 41.98 | 8.61 | 0 | 2.37E-06 | 5.52E-07 | 3.47E-06 | 5.71E-01 | rs7298467 | 3 |
| PCGF2 | 17 | 36890149 | 36904561 | 53.92 | 39.36 | 7.29 | 0 | 2.21E-06 | 1.15E-07 | 7.21E-03 | 1.44E-02 | rs3785457 | 2 |
| SLC9A8∘,¶ | 20 | 48429249 | 48508779 | 41.28 | 53.94 | 12.49 | 0 | 4.15E-07 | 1.33E-08 | 4.17E-03 | 1.91E-01 | rs17786105 | 10 |
| C-reactive protein (CRP) | Class-level score test | SNP-level score p-value | |||||||||||
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| Class | Chr | Start♯ | Stop♯ | 𝒞 | t̃t‡ | l | δ | p-value | Min | Median | Max | minP rs§ | # SNPs |
|
| |||||||||||||
| IKBKE¶ | 1 | 206643585 | 206670223 | 49.34 | 39.51 | 7.04 | 0 | 1.63E-06 | 5.93E-06 | 2.11E-03 | 1.14E-01 | rs4844539 | 7 |
| ENSG00000261000.1* | 1 | 206677280 | 206677789 | 80.45 | 30.23 | 4.00 | 0 | 4.40E-06 | 1.62E-06 | 9.42E-06 | 1.72E-05 | rs2871360 | 2 |
| ENSG00000224165.1* | 2 | 25194258 | 25262563 | 67.58 | 32.52 | 4.58 | 0 | 2.95E-06 | 1.77E-06 | 1.77E-06 | 6.01E-01 | rs4665750 | 16 |
| XLOC_002310*∘,¶ | 2 | 128193815 | 128228064 | 66.14 | 36.94 | 4.96 | 0 | 5.86E-07 | 4.36E-08 | 5.40E-05 | 4.71E-01 | rs11900469 | 12 |
| ENSG00000231731.3*,¶ | 2 | 128221217 | 128263373 | 59.89 | 35.71 | 5.37 | 0 | 1.62E-06 | 2.57E-07 | 5.40E-05 | 9.74E-01 | rs3889307 | 8 |
| ENSG00000272789.1* | 2 | 128383571 | 128384423 | 82.25 | 31.61 | 4.02 | 0 | 2.35E-06 | 1.78E-06 | 5.10E-06 | 8.41E-06 | rs13015157 | 2 |
| COL5A2∘,¶ | 2 | 189896640 | 190044605 | 112.49 | 56.22 | 4.46 | 0 | 3.48E-11 | 1.24E-10 | 2.02E-08 | 2.24E-06 | rs10931393 | 7 |
| XLOC_002433*,¶ | 2 | 190202502 | 190305828 | 91.57 | 35.49 | 4.03 | 0 | 3.82E-07 | 1.75E-07 | 1.75E-07 | 2.93E-05 | rs1520855 | 7 |
| WDR75¶ | 2 | 190306158 | 190340264 | 94.93 | 35.54 | 4.00 | 0 | 3.61E-07 | 1.75E-07 | 5.98E-07 | 1.02E-06 | rs13032853 | 2 |
| FAM134A | 2 | 220042938 | 220050197 | 78.80 | 30.10 | 4.01 | 0 | 4.73E-06 | 9.73E-07 | 2.23E-05 | 2.23E-05 | rs2385394 | 5 |
| TPRG1∘ | 3 | 188889762 | 189041271 | 30.44 | 57.91 | 17.04 | 0 | 2.38E-06 | 9.38E-09 | 1.87E-01 | 8.89E-01 | rs1515078 | 37 |
| ENSG00000248425.1* | 4 | 14392062 | 14395616 | 36.87 | 48.94 | 12.74 | 0 | 3.73E-06 | 1.57E-05 | 3.85E-02 | 2.24E-01 | rs2191685 | 7 |
| TCF21¶ | 6 | 134210258 | 134213393 | 64.02 | 41.16 | 5.60 | 0 | 1.74E-07 | 3.78E-07 | 3.13E-05 | 7.40E-01 | rs41286216 | 11 |
| C11orf95¶ | 11 | 63527363 | 63536113 | 100.93 | 37.42 | 4.00 | 4.21E-08 | 1.47E-07 | 1.47E-07 | 1.47E-07 | 1.47E-07 | rs2509744 | 2 |
| B3GAT1 | 11 | 134248397 | 134281812 | 34.07 | 51.13 | 14.15 | 0 | 4.39E-06 | 5.25E-07 | 3.30E-01 | 9.65E-01 | rs1866768 | 9 |
| TMEM132B¶ | 12 | 125811161 | 126143589 | 24.56 | 82.79 | 29.09 | 0 | 4.73E-07 | 1.19E-07 | 4.09E-01 | 9.99E-01 | rs7955449 | 84 |
| VASN¶ | 16 | 4421848 | 4433529 | 83.06 | 38.55 | 4.53 | 0 | 1.67E-07 | 4.46E-07 | 1.27E-05 | 2.50E-05 | rs3810818 | 2 |
| XLOC_012931*,¶ | 19 | 6656384 | 6662832 | 76.65 | 33.61 | 4.32 | 0 | 1.32E-06 | 4.89E-07 | 1.03E-04 | 2.05E-04 | rs344569 | 2 |
| CNBD2¶ | 20 | 34556528 | 34618622 | 78.90 | 33.07 | 4.11 | 0 | 1.33E-06 | 6.31E-07 | 5.79E-06 | 1.26E-04 | rs2590965 | 4 |
| ENSG00000226527.1*,¶ | 21 | 34484004 | 34496009 | 52.84 | 43.70 | 7.75 | 0 | 5.11E-07 | 8.68E-06 | 3.77E-03 | 6.56E-02 | rs11088239 | 6 |
Classes with at least two single nucleotide polymorphisms (SNPs) and a class-level score statistic p-value ≤ 5 × 10−6 are reported.
C11orf95 is also called ENSG00000188070.8 and ENSG00000224165.1 is also called XLOC_001398.
Classes additionally meeting the Bonferroni-corrected threshold of p ≤ 0.05/22, 949 = 2.18 × 10−6.
Class boundaries are extended by 5 Kb up and down stream from indicated start and stop locations in order to capture potentially associated regulatory elements.
t̃ = t* σχ + μχ.
lncRNAs while all other classes are protein-coding genes.
minP rs is the identifier for the SNP within the class with the smallest SNP-level score test p-value.
Classes that were identified as significantly associated with the corresponding biomarker based on the SNP-level score test as described in Table IV including extended boundaries (minimum SNP-level score p-value ≤ 5 × 10−8).