Table 4.
Genome-wide-Significant SNPs Localizing at the TSS of Phenotypically Relevant Mendelian Disorder Genes
| Complex Trait | SNP ID | Chromosomal Position | Z Score | Gene (MIM) | Maximum eQTL Effect | Maximum −log10 p Value | Tissues |
|---|---|---|---|---|---|---|---|
| PBC | rs13239597 | chr7: 128,695,982 | 9.85 | TNPO3 (610032) | – | – | – |
| HGT | rs8028537 | chr15: 89,345,946 | −9.33 | ACAN (155760) | – | – | – |
| HGT | rs10853751 | chr19: 41,903,219 | 8.71 | BCKDHA (608348) | – | – | – |
| CD | rs59283234 | chr5: 150,225,586 | −8.45 | IRGM (608212) | −0.042 | 6.733 | whole blood |
| CD | rs751627 | chr5: 150,225,112 | −8.45 | IRGM (608212) | −0.042 | 6.733 | whole blood |
| CD | rs35707106 | chr5: 150,225,376 | −8.33 | IRGM (608212) | −0.041 | 6.412 | whole blood |
| HGT | rs2298307 | chr6: 80,816,295 | 8.28 | BCKDHB (248611) | – | – | – |
| HGT | rs12386601 | chr7: 92,157,885 | 8.20 | PEX1 (602136) | – | – | – |
| BMI | rs17066842 | chr18: 58,040,623 | −7.54 | MC4R (155541) | – | – | – |
| HGT | rs12192268 | chr6: 110,011,457 | −7.00 | FIG4 (609390) | – | – | – |
| CAD | rs1332327 | chr10: 91,011,680 | 6.80 | LIPA (613497) | 12.541 | 5.132 | subcutaneous adipose, visceral adipose, adrenal gland, transverse colon, lung, spleen, thyroid, whole blood |
| RA | rs13239597 | chr7: 128,695,982 | 6.66 | TNPO3 (610032) | – | – | – |
| IBD | rs59283234 | chr5: 150,225,586 | 6.51 | IRGM (608212) | −0.042 | 6.733 | whole blood |
| IBD | rs751627 | chr5: 150,225,112 | 6.51 | IRGM (608212) | −0.042 | 6.733 | whole blood |
| HGT | rs7592246 | chr2: 219,926,220 | 6.45 | IHH (600726) | 0.056 | 6.199 | brain cerebellum |
| IBD | rs34005003 | chr5: 150,225,198 | 6.43 | IRGM (608212) | −0.043 | 6.637 | whole blood |
| IBD | rs35707106 | chr5: 150,225,376 | 6.33 | IRGM (608212) | −0.041 | 6.412 | whole blood |
| MNR | rs3775971 | chr4: 104,641,919 | 6.20 | TACR3 (162332) | −0.019 | 8.588 | lung |
| IBD | rs27741 | chr16: 28,504,180 | 6.11 | CLN3 (607042) | – | – | – |
| HGT | rs4244808 | chr11: 2,163,109 | 6.06 | IGF2 (147470) | – | – | – |
| RBC | rs1010222 | chr19: 13,048,607 | −5.96 | CALR (109091) | 17.142 | 6.851 | lung |
| CD | rs27741 | chr16: 28,504,180 | −5.87 | CLN3 (607042) | – | – | – |
| HGT | rs613924 | chr11: 65,769,294 | −5.86 | BANF1 (603811) | – | – | – |
| AFB | rs4845357 | chr1: 153,896,211 | −5.78 | GATAD2B (614998) | −0.108 | 4.443 | skin not exposed |
| HGT | rs6591226 | chr11: 66,675,989 | 5.52 | PC (608786) | – | – | – |
GWAS SNPs from the credible set for each complex trait were intersected with TSS regions 1 kb upstream of phenotypically matched Mendelian disorder genes. This table lists all genome-wide-significant SNPs (p < 5 × 10−8 from GWASs) with chromosomal location from all complex traits localizing at the TSS of a phenotypically matched Mendelian disorder gene.