Table 2.
The top hit probes identified in SMR analyses
| eQTL data | Probe | Gene | CHR | Top SNP | OR (95% CI) | PeQTL | PGWAS | Beta | SE | PSMR | PHEIDI | Q value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CAGE | ILMN_2150787 | HLA-C | 6 | rs2523578 | 1.14 (1.11–1.17) | 1.55 × 10− 65 | 2.62 × 10− 24 | − 0.2378 | 0.0272 | 2.10 × 10− 18 | 9.48 × 10− 12 | 5.73 × 10− 13 |
| ILMN_1682717 | IER3 | 6 | rs2233980 | 0.85 (0.83–0.88) | 2.05 × 10− 60 | 5.47 × 10− 22 | − 0.2065 | 0.0249 | 1.07 × 10− 16 | 1.89 × 10− 03 | 7.30 × 10− 12 | |
| ILMN_1661439 | FLOT1 | 6 | rs3130985 | 0.85 (0.83–0.88) | 6.93 × 10− 37 | 2.55 × 10− 22 | − 0.2666 | 0.0345 | 1.16 × 10− 14 | 2.68 × 10− 02 | 3.53 × 10− 10 | |
| ILMN_1700067 | BTN3A2 | 6 | rs9393710 | 0.89 (0.86–0.92) | 9.06 × 10− 237 | 3.86 × 10− 12 | 0.0832 | 0.0123 | 1.24 × 10− 11 | 9.13 × 10− 08 | 2.11 × 10− 07 | |
| ILMN_1820787 | BTN2A1 | 6 | rs3734544 | 0.91 (0.88–0.94) | 3.34 × 10− 189 | 1.40 × 10− 10 | − 0.0877 | 0.0140 | 3.60 × 10− 10 | 1.40 × 10− 08 | 3.93 × 10− 06 | |
| ILMN_1721113 | HLA-C | 6 | rs9266075 | 1.08 (1.05–1.1) | 2.99 × 10− 183 | 5.90 × 10− 10 | − 0.0867 | 0.0143 | 1.35 × 10− 09 | 1.12 × 10− 03 | 1.02 × 10− 05 | |
| ILMN_1803945 | HCP5 | 6 | rs2596495 | 0.85 (0.83–0.88) | 5.73 × 10− 14 | 1.58 × 10− 21 | 0.4716 | 0.0798 | 3.48 × 10− 09 | 3.20 × 10− 02 | 1.94 × 10− 05 | |
| ILMN_2044927 | RNF5 | 6 | rs192471087 | 0.91 (0.89–0.94) | 2.49 × 10− 37 | 1.28 × 10− 10 | − 0.1974 | 0.0343 | 8.59 × 10− 09 | 1.29 × 10− 04 | 3.00 × 10− 05 | |
| ILMN_1804571 | ZKSCAN4 | 6 | rs13200462 | 0.89 (0.86–0.92) | 2.61 × 10− 19 | 1.37 × 10− 13 | − 0.3193 | 0.0558 | 1.08 × 10− 08 | 1.88 × 10− 02 | 3.00 × 10− 05 | |
| ILMN_1660436 | HSPA1A | 6 | rs494620 | 1.07 (1.05–1.1) | 1.40 × 10− 74 | 1.81 × 10− 09 | 0.1417 | 0.0248 | 1.10 × 10− 08 | 2.16 × 10− 09 | 3.00 × 10− 05 | |
| GTEx | ENSG00000271581.1 | XXbac-BPG248L24.12 | 6 | rs9266244 | 1.14 (1.11–1.17) | 1.52 × 10− 16 | 2.96 × 10− 24 | 0.2043 | 0.0319 | 1.44 × 10− 10 | 4.34 × 10− 07 | 6.22 × 10− 06 |
| ENSG00000186470.9 | BTN3A2 | 6 | rs68112369 | 0.89 (0.86–0.92) | 9.15 × 10− 70 | 1.14 × 10− 11 | 0.1088 | 0.0172 | 2.28 × 10− 10 | 1.07 × 10− 03 | 6.22 × 10− 06 | |
| ENSG00000224389.4 | C4B | 6 | rs1270942 | 0.87 (0.84–0.9) | 3.63 × 10− 19 | 1.44 × 10− 16 | − 0.1233 | 0.0203 | 1.23 × 10− 09 | 5.84 × 10− 02 | 1.48 × 10− 05 | |
| ENSG00000244731.3 | C4A | 6 | rs116667074 | 0.87 (0.84–0.9) | 5.15 × 10− 19 | 1.67 × 10− 15 | 0.1382 | 0.0233 | 2.88 × 10− 09 | 1.08 × 10− 01 | 1.96 × 10− 05 | |
| ENSG00000214894.2 | LINC00243 | 6 | rs3094222 | 0.85 (0.83–0.88) | 8.03 × 10− 12 | 3.93 × 10− 22 | − 0.3086 | 0.0553 | 2.38 × 10− 08 | 5.63 × 10− 03 | 1.04 × 10− 04 | |
| ENSG00000204644.5 | ZFP57 | 6 | rs2747431 | 0.93 (0.91–0.96) | 2.03 × 10− 85 | 5.51 × 10− 08 | − 0.0566 | 0.0108 | 1.62 × 10− 07 | 7.31 × 10− 05 | 4.88 × 10− 04 | |
| ENSG00000204536.9 | CCHCR1 | 6 | rs1265087 | 0.93 (0.91–0.95) | 4.64 × 10− 22 | 1.01 × 10− 08 | − 0.2081 | 0.0423 | 8.60 × 10− 07 | 7.49 × 10− 04 | 1.91 × 10− 03 | |
| ENSG00000137312.10 | FLOT1 | 6 | rs3094222 | 0.85 (0.83–0.88) | 3.74 × 10− 08 | 3.93 × 10− 22 | − 1.3396 | 0.2802 | 1.74 × 10− 06 | 1.11 × 10− 02 | 2.49 × 10− 03 | |
| ENSG00000231852.2 | CYP21A2 | 6 | rs7763805 | 0.89 (0.86–0.92) | 2.24 × 10− 10 | 5.15 × 10− 13 | − 0.1665 | 0.0349 | 1.85 × 10− 06 | 3.40 × 10− 01 | 2.49 × 10− 03 | |
| ENSG00000204622.6 | HLA-J | 6 | rs1611336 | 1.07 (1.04–1.09) | 6.54 × 10− 20 | 8.13 × 10− 08 | 0.1162 | 0.0251 | 3.78 × 10− 06 | 4.10 × 10− 04 | 4.10 × 10− 03 |
For a full list of the significant probes identified in the SMR analyses, please see Additional file 1: Table S4. The GWAS summarized data were provided by the study of Sakaue et al. and can be downloaded at http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90018001-GCST90019000/GCST90018866/harmonised/. The CAGE and GTEx eQTL data can be downloaded at https://cnsgenomics.com/data/SMR/#eQTLsummarydata.
OR (95% CI) is the odds ratio and the corresponding 95% confidence interval for the top SNPs. PeQTL is the P value of the top associated cis-eQTL in the eQTL analysis, and PGWAS is the P value for the top associated cis-eQTL in the GWAS analysis. Beta is the estimated effect size in SMR analysis, SE is the corresponding standard error, PSMR is the P value for SMR analysis and PHEIDI is the P value for the HEIDI test
CAGE Consortium for the Architecture of Gene Expression, CHR chromosome, CI confidence interval, eQTL expression quantitative trait loci, GTEx Genotype-Tissue Expression, HEIDI heterogeneity in dependent instruments, OR odds ratio, SNP single-nucleotide polymorphism, SMR summary data-based Mendelian randomization, FDR false discovery rate, GWAS genome-wide association studies, IgAN immunoglobulin A nephropathy