Extended Data Fig. 10: Complementarity of molecular QTL (molQTL) in interpreting GWAS loci.
From: A compendium of genetic regulatory effects across pig tissues
a, Number of GWAS loci linked to cis-eQTL, cis-sQTL, cis-eeQTL, cis-lncQTL and cis-enQTL in 34 tissues based on four different integrative methods, including colocalization (fastEnloc), Mendelian randomization (SMR), single-tissue transcriptome-wide association studies (TWAS, S-PrediXcan) and multi-tissue TWAS (S-MultiXcan). The bottom point-line combinations of the Upset plot represent the intersections of GWAS loci linked to eGenes by different types of molecular phenotypes. b, Distribution of rank correlations between tissue-relevance-scores derived from cis-eQTL and those from cis-sQTL, cis-lncQTL, cis-eeQTL and cis-enQTL across 86 GWAS traits with significant colocalizations for at least one molecular phenotype. c, Significant SMR signals (PSMR = 9.16 × 10−5, PHEIDI = 0.9) between GWAS loci of average daily gain (ADG) and cis-eQTL of CFAP298-TCP10L in colon, but not for its cis-sQTL or cis-eeQTL. The orange triangle represents the top cis-eQTL of CFAP298-TCP10L. d, Significant SMR signals (PSMR = 1.78 × 10−5, PHEIDI = 0.07) between GWAS loci of the average backfat thickness (BFT) and cis-sQTL of MYO7B in the small intestine, but not for its cis-eQTL or cis-eeQTL. e, Significant SMR signals (PSMR = 1.78 × 10−6, PHEIDI = 0.97) between GWAS loci of litter weight (LW, piglets born alive) and cis-eeQTL of FBXL12 in the uterus, but not for its cis-eQTL or cis-sQTL. f, Significant SMR signals (PSMR(lncQTL-GWAS) = 4.49 × 10−7, PSMR(eQTL-GWAS) = 5.45 × 10−5, PSMR(lncQTL-eQTL) = 4.62 × 10−7) among GWAS loci of loin muscle depth (LMD), cis-lncQTL of MSTRG.4694&ENSSSCT00000070888, and cis-eQTL of GOSR2 in the muscle. MSTRG.4694&ENSSSCT00000070888 is a lncRNA gene located on the 3112 bp downstream of GOSR2, where the Pearson’s correlation of their normalized expression levels (trimmed mean of M-value, TMM) is 0.29 in muscle. The orange and green triangles in the top GWAS Manhattan plot represent the top molQTL of GOSR2 and MSTRG.4694&ENSSSCT00000070888, respectively.
