Table 1. Most significant multi-tissue cis-eQTL for each associated eGene.
| eGene | Gene Function | eQTL | Alleles† | eQTL Location | β ± se | pmeta | FDR | Associated Disease(s) |
|---|---|---|---|---|---|---|---|---|
| CHRNA5 | Ligand-gated ion channel | rs12438181 | G/A | Chr 15, AGPHD1 intron | 0.28 ± 0.03 | 2.44E-27 | 1.75E-21 | SCZ |
| LINC00499 | Non-coding RNA | rs139708473 | G/A | Chr 4, LINC00499 intron | -0.51 ± 0.06 | 2.72E-19 | 3.69E-15 | MDD |
| ZNF603P | Non-coding RNA | rs156737 | A/G | Chr 6, intergenic | -0.4 ± 0.05 | 6.66E-18 | 7.27E-14 | SCZ |
| WBP2NL | Sperm-specific WW domain-binding protein | rs28439297 | C/T | Chr 22, NDUFA6-AS1 intron | -0.13 ± 0.02 | 1.11E-17 | 1.17E-13 | SCZ |
| HPR | Hemoglobin binding | rs8043723 | C/T | Chr 17, intergenic | -0.21 ± 0.03 | 9.26E-17 | 7.63E-13 | MDD |
| PCDHA10 | Calcium-dependent cell-adhesion | rs13168514 | G/T | Chr 5, intergenic | -0.28 ± 0.03 | 7.08E-16 | 5.53E-12 | SCZ, MDD |
| ZSCAN31 | Transcription factor | rs276362 | A/C | Chr 6, intergenic | -0.17 ± 0.02 | 4.98E-15 | 3.51E-11 | SCZ |
| HIST1H3E | Nucleosome component | rs67575965 | A/G | Chr 6, intergenic | -0.27 ± 0.04 | 1.27E-13 | 5.43E-10 | SCZ |
| BTN3A2 | Immunoglobin superfamily | rs3752417 | G/C | Chr 6, HIST1H3C synonmous variant | 0.15 ± 0.02 | 1.65E-13 | 6.61E-10 | SCZ, CD |
| C6orf3 | Non-coding RNA | rs6912446 | T/A | Chr 6, TRAF3IP2 intron | 0.16 ± 0.02 | 2.68E-13 | 1.04E-09 | SCZ |
| SMIM2-AS1 | Non-coding RNA | rs4432167 | G/C | Chr 13, intergenic | -0.21 ± 0.03 | 1.15E-12 | 3.77E-09 | CD |
| SRD5A3 | Steroid 5-alpha and polyprenol reductase families | rs2087319 | C/A | Chr 4, intergenic | -0.15 ± 0.02 | 1.89E-12 | 5.63E-09 | MDD |
| SRR | Catalyzes the synthesis of D-serine | rs4606747 | T/C | Chr 17, SRR intron | -0.17 ± 0.02 | 1.00E-11 | 2.21E-08 | SCZ |
| AC068039.4 | Non-coding RNA | rs6738445 | C/T | Chr 2, DYNC1I2 intron | -0.47 ± 0.07 | 5.38E-11 | 9.02E-08 | SCZ |
| LINC01184 | Non-coding RNA | rs36694 | A/C | Chr 5, intergenic | 0.12 ± 0.02 | 1.30E-10 | 2.01E-07 | BPD |
| RRN3 | Transcription initiation | rs4985147 | C/T | Chr 16, intron in RRN3 and PDXDC1 | -0.1 ± 0.02 | 1.66E-10 | 2.49E-07 | SCZ |
| GAS8 | Cytoskeletal linker | rs4785709 | G/A | Chr 16, ZNF276 intron | 0.08 ± 0.01 | 3.87E-10 | 4.99E-07 | BPD, CD |
| MASTL | Serine/threonine kinase | rs7080612 | G/T | Chr 10, ANKRD26 intron | 0.16 ± 0.03 | 4.07E-10 | 5.06E-07 | SCZ |
| TYW5 | tRNA hydroxylase | rs1704190 | A/G | Chr 2, intergenic | 0.1 ± 0.02 | 4.32E-10 | 5.18E-07 | SCZ |
| CD46 | Cofactor of complement factor I | rs1318653 | T/C | Chr 1, intergenic | 0.22 ± 0.04 | 8.63E-10 | 9.20E-07 | SCZ |
| RP11-275H4.1 | Non-coding RNA | rs1878874 | A/T | Chr 3, SOX2-OT intron | -0.19 ± 0.03 | 1.07E-09 | 1.12E-06 | SCZ |
| RSRC1 | Pre-mRNA splicing | rs12491598 | C/A | Chr 3, AK097794 non-coding variant | 0.11 ± 0.02 | 1.51E-09 | 1.48E-06 | MDD |
| LOC100130345 | Protein coding of unclear function | rs832190 | T/C | Chr 3, THOC7 intron | -0.1 ± 0.02 | 1.65E-09 | 1.55E-06 | SCZ |
| DDHD2 | Phospholipase enzyme | rs11779986 | A/G | Chr 8, BAG4 intron | -0.13 ± 0.02 | 1.75E-09 | 1.57E-06 | SCZ, CD |
| ZNF155 | Gene expression | rs1233454 | G/A | Chr 19, ZNF235 intron | 0.11 ± 0.02 | 2.88E-09 | 2.43E-06 | SCZ |
| LRRC37A15P | Non-coding RNA | rs223340 | A/G | Chr 4, UBE2D3 intron | -0.13 ± 0.02 | 4.40E-09 | 3.46E-06 | SCZ |
| HIST1H4H | Nucleosome component | rs198855 | T/A | Chr 6, intergenic | 0.12 ± 0.02 | 5.85E-09 | 4.16E-06 | SCZ |
| ADAMTSL3 | Peptidase activity | rs4842841 | G/A | Chr 15, ADAMTSL3 intron | 0.1 ± 0.02 | 6.37E-09 | 4.41E-06 | SCZ |
| LMAN2L | Early secretory pathway | rs878919 | T/C | Chr 2, CNNM4 intron | -0.1 ± 0.02 | 9.00E-09 | 5.98E-06 | BPD |
| ALMS1P | Non-coding RNA | rs11893881 | T/A | Chr 2, ALMS1 intron | -0.14 ± 0.02 | 1.52E-08 | 9.02E-06 | SCZ |
| MAU2 | Association of cohesion complex with chromatin during interphase | rs1009136 | G/A | Chr 19, MAU2 intron | 0.06 ± 0.01 | 1.58E-08 | 9.34E-06 | SCZ |
| RP11-776H12.1 | Non-coding RNA | rs7525211 | A/T | Chr 1, intergenic | 0.12 ± 0.02 | 1.67E-08 | 9.76E-06 | BPD |
| TMEM81 | Protein coding of unclear function | rs12143085 | A/G | Chr 1, RBBP5 intron | 0.16 ± 0.03 | 1.87E-08 | 1.07E-05 | SCZ |
| RP11-3N2.13 | Non-coding RNA | rs10257979 | A/C | Chr 7, ZNF727 intron | 0.18 ± 0.03 | 1.92E-08 | 1.10E-05 | SCZ |
| SPATA7 | Photoreceptor cell maintenance | rs11623942 | G/C | Chr 14, intergenic | 0.12 ± 0.02 | 1.94E-08 | 1.11E-05 | SCZ |
| ATP5G2 | Mitochondrial ATP synthase subunit | rs10876460 | A/G | Chr 12, PCBP2 intron | 0.09 ± 0.02 | 2.04E-08 | 1.15E-05 | SCZ |
| AF131216.5 | Non-coding RNA | rs11249996 | A/C | Chr 8, MSRA intron | -0.07 ± 0.01 | 2.24E-08 | 1.24E-05 | SCZ |
| MNT | Transcriptional repressor | rs413016 | C/T | Chr 17, TSR1 intron | -0.08 ± 0.02 | 2.80E-08 | 1.46E-05 | SCZ |
| GSTO2 | Glutathione-dependent thiol transferase activity | rs4925 | C/A | Chr 10, GSTO1 missense variant | 0.21 ± 0.04 | 3.35E-08 | 1.67E-05 | SCZ |
| TOM1L2 | Vesicular trafficking | rs11652881 | A/G | Chr 17, RAI1 intron | 0.09 ± 0.02 | 4.19E-08 | 1.95E-05 | SCZ |
†First allele listed is the reference allele for effect size. For example, relative to G, A has a β of 0.28 ± 0.03 EU per allele with respect to expression levels of CHRNA5.