Table 1.
Eighteen previous reported candidate target genes of GWAS-identified prostate cancer risk variants based on fine-mapping or eQTL
| Gene | Region | Classification | R2a | OR (95% CI) | P-value | P-value after FDRa | Closest risk SNPsb | Model | Reference (PMID) |
|---|---|---|---|---|---|---|---|---|---|
| SV2A | 1q21.2 | protein_coding | 0.02 | 0.9 (0.86-0.95) | 4.39×10−5 | 2.60×10−3 | rs56391074 | PrediXcan | 26611117 |
| RN7SL832P | 2p25.1 | lncRNA | 0.03 | 0.73 (0.67-0.79) | 9.99×10−14 | 3.19×10−11 | rs9287719 | Modified UTMOST | 27526323 |
| 0.08 | 0.9 (0.86-0.94) | 8.94×10−7 | 8.81×10−5 | rs9287719 | JTI | ||||
| EFHD1 | 2q37.1 | protein_coding | 0.12 | 0.89 (0.84-0.93) | 3.79×10−6 | 3.23×10−4 | rs59308963 | PrediXcan | 27409348 |
| 0.13 | 0.9 (0.86-0.94) | 9.29×10−6 | 6.84×10−4 | rs59308963 | Modified UTMOST | ||||
| 0.14 | 0.9 (0.86-0.94) | 2.46×10−6 | 2.22×10−4 | rs59308963 | JTI | ||||
| HDLBP | 2q37.3 | protein_coding | 0.03 | 1.09 (1.04-1.14) | 4.30×10−4 | 1.57×10−2 | rs111770284 | JTI | 24907074 |
| HLA-DQA2 | 6p21.32 | protein_coding | 0.62 | 1.04 (1.03-1.06) | 1.33×10−6 | 1.27×10−4 | rs9296068 | PrediXcan | 26611117 |
| 0.63 | 1.04 (1.02-1.06) | 2.71×10−5 | 1.72×10−3 | rs9296068 | Modified UTMOST | ||||
| 0.64 | 1.04 (1.02-1.05) | 8.36×10−6 | 6.22×10−4 | rs9296068 | JTI | ||||
| HLA-DRB1 | 6p21.32 | protein_coding | 0.17 | 0.9 (0.87-0.94) | 4.19×10−7 | 4.62×10−5 | rs3129859 | PrediXcan | 26611117 |
| NOTCH4 | 6p21.32 | protein_coding | 0.13 | 1.06 (1.03-1.1) | 5.28×10−4 | 1.84×10−2 | rs3096702 | PrediXcan | 26611117 |
| 0.2 | 1.06 (1.02-1.09) | 6.86×10−4 | 2.25×10−2 | rs3096702 | Modified UTMOST | ||||
| 0.24 | 1.05 (1.02-1.08) | 9.94×10−4 | 2.97×10−2 | rs3096702 | JTI | ||||
| HLA-C | 6p21.33 | protein_coding | 0.22 | 0.96 (0.94-0.98) | 4.50×10−4 | 1.63×10−2 | rs2596546 | PrediXcan | 26611117 |
| MICA | 6p21.33 | protein_coding | 0.51 | 1.03 (1.01-1.05) | 1.21×10−3 | 3.45×10−2 | rs2596546 | JTI | 26611117 |
| HOTTIP | 7p15.2 | lncRNA | 0.05 | 0.77 (0.71-0.83) | 2.19×10−10 | 4.28×10−8 | rs200362064 | JTI | 26611117 |
| RAB14 | 9q33.2 | protein_coding | 0.04 | 1.26 (1.1-1.43) | 5.60×10−4 | 1.93×10−2 | rs1571801 | Modified UTMOST | 25371445 |
| PSMB7 | 9q33.3 | protein_coding | 0.02 | 0.89 (0.84-0.95) | 1.01×10−4 | 5.04×10−3 | rs1571801 | JTI | 27409348 |
| AS3MT | 10q24.32 | protein_coding | 0.43 | 1.04 (1.02-1.06) | 6.84×10−4 | 2.25×10−2 | rs34032774 | PrediXcan | 26611117, 26162851, 24907074 |
| 0.46 | 1.04 (1.02-1.06) | 4.46×10−4 | 1.61×10−2 | rs34032774 | Modified UTMOST | ||||
| 0.48 | 1.03 (1.01-1.05) | 4.08×10−4 | 1.52×10−2 | rs34032774 | JTI | ||||
| NT5C2 | 10q24.32-33 | protein_coding | 0.02 | 1.24 (1.16-1.33) | 8.67×10−11 | 1.84×10−8 | rs34032774 | Modified UTMOST | 26611117 |
| C1QL4 | 12q13.12 | protein_coding | 0.25 | 1.09 (1.06-1.13) | 6.21×10−8 | 8.50×10−6 | rs10875943 | PrediXcan | 24907074 |
| 0.26 | 1.1 (1.06-1.14) | 5.66×10−7 | 6.05×10−5 | rs10875943 | Modified UTMOST | ||||
| 0.25 | 1.09 (1.05-1.12) | 1.17×10−7 | 1.48×10−5 | rs10875943 | JTI | ||||
| C14orf39 | 14q23.1 | protein_coding | 0.06 | 0.87 (0.8-0.94) | 9.71×10−4 | 2.92×10−2 | rs7153648 | PrediXcan | 26611117 |
| 0.11 | 0.9 (0.84-0.96) | 1.48×10−3 | 3.99×10−2 | rs7153648 | JTI | ||||
| SYNJ2BP | 14q24.2 | protein_coding | 0.07 | 1.25 (1.16-1.36) | 3.82×10−8 | 5.54×10−6 | rs7141529 | Modified UTMOST | 26611117 |
| 0.08 | 1.2 (1.12-1.28) | 1.65×10−7 | 2.05×10−5 | rs7141529 | JTI | ||||
| ZNF652 | 17q21.32 | protein_coding | 0.04 | 1.36 (1.16-1.6) | 1.89×10−4 | 8.26×10−3 | rs11650494 | JTI | 26162851, 26025378, 24907074 |
a
R2: prediction performance (R2) derived using GTEx data. P value: derived from association analyses of 79,194 cases and 61,112 controls; associations with FDR-corrected P value ≤ 0.05 considered significant
b
Risk SNPs identified in previous GWAS or fine-mapping studies. The risk SNP closest to the gene is presented.
lncRNA: long noncoding RNAs.