Table 1D.
Novel shared genomic regions shared between choice for instant coffee and T2DM or T2DM-related phenotypes.
| T2DM/related phenotypes | CHR | N | POS | KB | Index SNP | A1 | A2 | Coffee type | T2DM/related phenotype | CPASSOC | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| beta | p | beta | p | p | ||||||||
| T2DM | 1 | 1 | chr1:112277693-112277693 | 0.001 | rs127204 | C | A | 0.0152 | 4.32E-03 | 0.0320 | 1.00E-06 | 3.45E-08 |
| 1 | 6 | chr1:26726127-26743903 | 17.777 | rs113466616 | A | G | 0.0170 | 2.12E-03 | 0.0350 | 1.80E-07 | 5.92E-09 | |
| 1 | 1 | chr1:229594310-229594310 | 0.001 | rs10916480 | G | A | 0.0161 | 3.49E-02 | 0.0510 | 6.10E-08 | 1.27E-08 | |
| 2 | 1 | chr2:165770457-165770457 | 0.001 | rs16849922 | C | A | -0.0122 | 2.40E-02 | 0.0330 | 3.30E-07 | 3.45E-08 | |
| 2 | 4 | chr2:161354368-161368808 | 14.441 | rs79523138 | G | A | -0.0187 | 1.96E-02 | 0.0540 | 5.20E-08 | 3.05E-09 | |
| 4 | 17 | chr4:157676228-157745957 | 69.73 | rs4691382 | G | A | -0.0150 | 1.33E-02 | -0.0400 | 9.80E-08 | 6.78E-09 | |
| 5 | 1 | chr5:59398807-59398807 | 0.001 | rs73759013 | C | A | -0.0188 | 4.67E-03 | -0.0410 | 3.10E-07 | 2.53E-08 | |
| 6 | 3 | chr6:153367613-153391618 | 24.006 | rs7767938 | C | T | 0.0192 | 1.55E-03 | 0.0360 | 9.60E-07 | 2.77E-08 | |
| 7 | 2 | chr7:104415434-104420060 | 4.627 | rs4460308 | C | T | 0.0176 | 1.23E-03 | 0.0330 | 1.00E-06 | 1.63E-08 | |
| 7 | 1 | chr7:28222877-28222877 | 0.001 | rs139048357 | A | C | 0.0566 | 1.49E-02 | -0.1600 | 4.60E-07 | 1.41E-08 | |
| 7 | 1 | chr7:74134911-74134911 | 0.001 | rs35005436 | C | T | 0.0174 | 1.52E-02 | 0.0470 | 2.50E-07 | 3.08E-08 | |
| 8 | 4 | chr8:19780310-19808131 | 27.822 | rs113023641 | A | G | -0.0212 | 4.70E-03 | -0.0480 | 1.50E-07 | 1.02E-08 | |
| 9 | 1 | chr9:19093017-19093017 | 0.001 | rs10963961 | G | C | -0.0116 | 4.68E-02 | 0.0360 | 4.40E-07 | 4.34E-08 | |
| 9 | 8 | chr9:97772285-97795176 | 22.892 | rs10993460 | C | T | 0.0238 | 9.79E-03 | -0.0580 | 3.00E-07 | 5.10E-09 | |
| 11 | 3 | chr11:45875392-45877688 | 2.297 | rs7951225 | T | A | -0.0155 | 1.70E-02 | -0.0410 | 2.50E-07 | 2.89E-08 | |
| 12 | 19 | chr12:4237568-4257553 | 19.986 | rs113966250 | G | C | -0.0385 | 3.17E-02 | -0.1200 | 7.00E-08 | 2.04E-09 | |
| 14 | 3 | chr14:69446960-69447386 | 0.427 | rs8016537 | A | G | 0.0164 | 1.81E-03 | 0.0310 | 1.00E-06 | 3.22E-08 | |
| 14 | 2 | chr14:101309692-101309759 | 0.068 | rs2295388 | A | G | 0.0154 | 1.56E-02 | -0.0390 | 3.70E-07 | 1.75E-08 | |
| 17 | 1 | chr17:37402280-37402280 | 0.001 | rs2100651 | A | C | -0.0198 | 9.53E-04 | -0.0350 | 2.00E-06 | 4.62E-08 | |
| 17 | 2 | chr17:17612187-17739163 | 126.977 | rs77745346 | T | C | -0.0234 | 4.17E-02 | 0.0700 | 1.60E-07 | 9.42E-09 | |
| 19 | 9 | chr19:13139616-13212025 | 72.41 | rs12151248 | T | C | 0.0274 | 7.43E-04 | -0.0520 | 4.10E-07 | 1.18E-09 | |
| BMI | 3 | 1 | chr3:66668365-66668365 | 0.001 | rs11128158 | G | A | -0.012 | 3.40E-02 | 0.010 | 1.10E-07 | 7.94E-09 |
| 4 | 2 | chr4:81194090-81199966 | 5.877 | rs3796606 | G | A | 0.016 | 3.52E-03 | -0.008 | 2.70E-06 | 4.73E-08 | |
| 7 | 2 | chr7:104435213-104441909 | 6.697 | rs2470961 | A | G | 0.020 | 2.02E-04 | 0.008 | 4.60E-06 | 3.28E-08 | |
| 10 | 4 | chr10:124929763-124947286 | 17.524 | rs12218544 | C | G | 0.019 | 2.05E-02 | -0.014 | 1.40E-07 | 4.29E-09 | |
| 12 | 1 | chr12:117630765-117630765 | 0.001 | rs4492907 | C | T | 0.011 | 3.13E-02 | 0.009 | 1.00E-07 | 2.34E-08 | |
| 12 | 6 | chr12:84242417-84306965 | 64.549 | rs922160 | G | A | 0.016 | 2.76E-03 | 0.009 | 3.90E-07 | 1.93E-08 | |
| 16 | 1 | chr16:54120330-54120330 | 0.001 | rs10492872 | G | T | -0.013 | 1.75E-02 | 0.009 | 1.30E-06 | 2.43E-08 | |
| 17 | 1 | chr17:35061859-35061859 | 0.001 | rs6607342 | C | T | 0.017 | 2.53E-02 | 0.013 | 1.20E-07 | 4.55E-08 | |
| 18 | 1 | chr18:73122598-73122598 | 0.001 | rs11660753 | A | G | 0.013 | 2.18E-02 | -0.009 | 4.90E-07 | 4.22E-08 | |
| 20 | 5 | chr20:50403227-50505843 | 102.617 | rs6021437 | C | T | -0.016 | 4.41E-03 | -0.010 | 9.90E-08 | 5.73E-09 | |
| 20 | 1 | chr20:8352693-8352693 | 0.001 | rs6086425 | G | A | 0.016 | 2.16E-02 | -0.011 | 3.30E-07 | 1.10E-08 | |
POS, position of shared genomic regions; A1, effect allele of index SNP; A2, non-effect allele of index SNP; CPASSOC, cross-phenotype association analysis using R package “CPASSOC”; T2DM, type 2 diabetes mellitus; BMI, body mass index.