Table 2.
Top 10 ranked Matsuda insulin sensitivity–correlated cis-eGenes in adipose tissue from African American (AAGMEx cohort) and European ancestry (METSIM) individuals
| Gene symbol | Chr | AAGMEx cohort |
METSIM cohort |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Matsuda insulin sensitivity index |
eQTL analysis |
Matsuda insulin sensitivity index |
eQTL analysis |
||||||||||||||
| ρ | P | Probe ID | Top cis-eSNP | A1 | MAF | β* | eQTL_ P value | β | P value | Probeset ID | Top cis-eSNP | alt_ allele | MAF | β* | eQTL_ P value | ||
| ECHDC3 | 10 | 0.471 | 5.33E-15 | ILMN_2072178 | rs200943982 | T | 0.401 | −0.281 | 1.94E-09 | 0.342 | 2.35E-22 | 11728810_a_at | rs3814627 | G | 0.312 | −0.755 | 8.3E-52 |
| MIF | 22 | −0.390 | 2.26E-10 | ILMN_1807074 | rs4822455 | T | 0.435 | −0.188 | 4.56E-13 | −0.257 | 5.64E-13 | 11744470_x_at | rs4822443 | A | 0.225 | −0.989 | 1.3E-78 |
| CENPV | 17 | 0.411 | 1.86E-11 | ILMN_3246608 | rs3112521 | T | 0.427 | 0.107 | 5.83E-09 | 0.288 | 4.85E-16 | 11722721_a_at | rs3112526 | C | 0.485 | 0.751 | 2.3E-53 |
| DDT | 22 | 0.362 | 4.71E-09 | ILMN_1690982 | rs79966373 | G | 0.178 | −0.302 | 2.81E-14 | 0.277 | 5.30E-15 | 11731089_a_at | chr22:24334948 | C | 0.353 | −1.055 | 1E-125 |
| APOB | 2 | 0.401 | 6.50E-11 | ILMN_1664024 | rs1429974 | T | 0.241 | 0.293 | 5.28E-09 | 0.256 | 7.13E-13 | 11758033_s_at | rs11693870 | C | 0.265 | 0.950 | 9E-72 |
| ORMDL3 | 17 | 0.445 | 2.24E-13 | ILMN_1662174 | rs28820390 | A | 0.091 | −0.355 | 3.37E-07 | 0.392 | 1.52E-29 | 11736188_a_at | rs2872516 | T | 0.495 | −0.565 | 1.2E-29 |
| GLIPR1 | 12 | −0.458 | 3.55E-14 | ILMN_1769245 | rs117251563 | A | 0.013 | 0.705 | 8.07E-07 | −0.217 | 1.30E-09 | 11721839_at | rs35619460 | C | 0.194 | −1.445 | 1E-158 |
| ACSS3 | 12 | 0.449 | 1.32E-13 | ILMN_1659885 | rs4842386 | G | 0.167 | −0.111 | 6.97E-06 | 0.332 | 2.99E-21 | 11759049_at | rs3794325 | A | 0.332 | −0.919 | 5.9E-81 |
| ITIH5 | 10 | −0.434 | 9.54E-13 | ILMN_1731862 | rs201694044 | G | 0.375 | −0.154 | 5.05E-07 | −0.325 | 2.66E-20 | 11734677_x_at | rs867490 | G | 0.312 | 0.610 | 6.8E-33 |
| DMRT2 | 9 | 0.401 | 6.05E-11 | ILMN_1751785 | rs756145 | G | 0.315 | 0.282 | 2.77E-08 | 0.300 | 1.80E-17 | 11727728_a_at | rs10959032 | T | 0.271 | −0.699 | 9.4E-37 |
Matsuda insulin sensitivity–correlated transcripts of Entrez ID genes in adipose tissue associated with a SNP (q value <0.04) within ±500 Kb of the 5′ and 3′ end of the transcript in AAGMEx are shown. Data for most significantly associated genotyped cis-eSNP in AAGMEx are presented. Data on European ancestry males are from the METSIM cohort (Civelek et al. [20]). In AAGMEx: ρ, Spearman partial correlation coefficient; P value, significance level of correlation of transcript level with Matsuda index in Spearman partial correlation analysis; A1, minor allele; β, effect size of minor allele (A1); eQTL_P value, significance in additive model (in MatrixEQTL analysis). In METSIM: β, β value; P value, significance level of correlation of transcript level with Matsuda index in linear regression analysis; alt_allele, alternative allele; β*, effect size for alternative allele of best cis-eSNP in FaST-LMM eQTL analysis. Results for all significant probes are shown in Supplementary Table 4. Top cis-eSNPs are not the same in both cohorts, but comparison of their effects is shown in Supplementary Table 4A and B and in Supplementary Fig. 3. Chr, chromosome.