Table 1
| GWAS locus gene name* | GWAS trait (s)* | GWAS SNP* | GWAS risk/higher trait level allele* | GWAS OR/ effect size*† | eQTL effect size‡ | eQTL gene | MESI decile§ | eQTL q-value | eQTL conditional q-value|| |
|---|---|---|---|---|---|---|---|---|---|
| ERAP2 | 2-h glucose | rs1019503 | A | 0.063 | 1.16 | ERAP2 | 3 | 2.1 × 10−62 | 7.0 × 10−84 |
| ERAP2 | 2-h glucose | rs1019503 | A | 0.063 | −0.97 | LNPEP | 7 | 8.1 × 10−36 | 7.8 × 10−39 |
| ERAP2 | 2-h glucose | rs1019503 | A | 0.063 | −0.90 | CTD-2260A17.2 | 7 | 1.1 × 10−28 | 4.4 × 10−33 |
| AMT | Fasting glucose | rs11715915 | C | 0.012 | −0.61 | AMT | 1 | 1.3 × 10−10 | 5.8 × 10−32 |
| ANK1 | T2D | rs515071 | C | 1.18 | 1.01 | ANK1 | 10 | 1.9 × 10−19 | 2.0 × 10−24 |
| ANK1¶ | T2D | rs516946 | C | 1.09 | 1.01 | ANK1 | 10 | 1.9 × 10−19 | 2.0 × 10−24 |
| FADS1, FADS1-2-3 | Fasting glucose | rs174550 | T | 0.022 | 0.77 | FADS1 | 3 | 4.2 × 10−18 | 3.2 × 10−20 |
| POU5F1/TCF19 | T2D | rs3132524 | G | 1.07 | −0.84 | CCHCR1 | 9 | 4.2 × 10−17 | 1.2 × 10−19 |
| POU5F1/TCF19 | T2D | rs3132524 | G | 1.07 | 0.79 | HCG27 | 2 | 4.6 × 10−15 | 1.9 × 10−14 |
| AMT | Fasting glucose | rs11715915 | C | 0.012 | −0.68 | NICN1 | 5 | 1.6 × 10−13 | 1.4 × 10−13 |
| JAZF1 | T2D | rs849135 | G | 1.11 | −0.38 | JAZF1 | 4 | 5.3 × 10−4 | 5.6 × 10−11 |
| KCNJ11 | T2D | rs5215 | C | 1.07 | −0.33 | ABCC8 | NA | 1.5 × 10−2 | 1.4 × 10−10 |
| GPSM1 | T2D | rs11787792 | A | 1.15 | 0.38 | GPSM1 | 1 | 1.9 × 10−3 | 6.7 × 10−10 |
| PROX1 | Fasting glucose | rs340874 | C | 0.021 | 0.49 | PROX1-AS1 | 3 | 1.3 × 10−6 | 7.5 × 10−10 |
| PROX1 | T2D | rs340874 | C | 1.07 | 0.49 | PROX1-AS1 | 3 | 1.3 × 10−6 | 7.5 × 10−10 |
| ZFAND3 | T2D | rs9470794 | C | 1.12 | 0.90 | ZFAND3 | 9 | 5.1 × 10−8 | 1.4 × 10−9 |
2-h, 2 hour; eQTL, expression quantitative trait locus; GWAS, genome-wide association studies; SNP, single-nucleotide polymorphism; T2D, type 2 diabetes; TSS, transcription start site.
T2D and related trait GWAS and candidate gene-associated variants were tested for association with genes whose most distal TSS was within 1 Mb of the variant.
*We use GWAS to denote GWAS or candidate gene studies.
†T2D odds ratio (OR) or trait effect size for GWAS risk or higher trait level allele.
‡eQTL effect for GWAS risk or higher trait level allele.
§Decile 10 denotes most muscle-specific expression, NA denotes insufficient expression in the Illumina Body Map tissues to estimate specificity.
||15 most significant conditional cis-eQTL results (for the 4,545 tested GWAS-SNP–gene pairs) that also have an cis-eQTL q-value<0.05 (genome-wide).
¶See Supplementary Data 1 for ANK1 SNP rs515071 (high r2 with rs516946).