Table 2.
Summary of colocalization and SMR analyses of retina eQTL, mQTL and AMD associations
| Method | mQTL -> eQTL | eQTL -> mQTL | eQTL -> AMD GWAS | mQTL -> AMD GWAS | mQTL <-> eQTL <-> AMD GWAS |
|---|---|---|---|---|---|
| SMRa | 6592 associations (5175 mQTLs, 5012 eQTLs) and 2101 genes (232 eQTMs) | 5805 associations (2256 eQTLs, 5612 mQTLs) and 1983 genes (Common with mQTL->eQTL: 554 associations,1447 genes) | 8 associations, 5 GWAS loci (CFI, C2/CFB/SKIV2L, PILRB/PILRA, RDH5/CD63, TMEM97/VTN) | 5 associations, 3 GWAS loci (KMT2E/SRPK2, PILRB/PILRA, ARMS2/HTRA1) | - |
| coloc | 9417 variants and 2423 genes (343 associations and 177 genes common with SMR eQTL -> mQTL) | 9417 variants and 2423 genes (343 associations and 177 genes common with SMR eQTL -> mQTL) | 44 eVariants and 32 genes at 3 AMD loci; 47 new AMD associations (29 eVariants and 24 genes) | 69 mVariants, 81 CpG sites corresponding to 58 genes, at 11 AMD loci; 42 new AMD associations (36 mVariants and 43 CpG sites corresponding to 30 genes) | 3 colocalizing variants, but different target genes overlapped between eQTL -> AMD GWAS and mQTL -> AMD GWAS, at 3 AMD loci (PILRB/PILRA, TMEM97/VTN, and CNN2). |
| eCAVIAR | - | - | 5 loci (2 loci colocalizing only with eQTL: SARM1 and TMEM199 target genes at TMEM97/VTN locus and TMEM259 at CNN2 locus) | 8 loci (5 loci colocalizing only with mQTL: CFH as target gene at CFH locus, LINC01004 at KMT2E/SRPK2 locus, ARHGAP21 and RNA5SP305 at ARHGAP2 locus, RAD51B at RAD51B locus, and MARK4 at APOE(EXOC3L2/MARK4) locus) | - |
| moloc | - | - | - | - | 18 colocalizing eQTL and mQTL variants for 18 CpG sites and 10 genes in 3 known AMD loci (DXO in locus C2/CFB/SKIV2L, AP4M1 in locus PILRB/PILRA and TMEM259 in locus CNN2) and 7 new AMD associations |
aSMR results that pass HEIDI linkage test P > 0.05.