Table 2.
G × Cell-Proportion Interactions Identify Cell-Type-Specific eQTLs from Bulk Adipose-Tissue Gene-Expression Profiles
| Cell Type | SNP | Gene | β | p Value | Fairfax et al. Stimulus & Proxy SNP | GTEx Top eQTL Tissues | Regulatory Regions |
|---|---|---|---|---|---|---|---|
| macrophage | rs61913538 | CLEC12A | 0.37 | 8.4 × 10−25 | naive, rs7313235 | WB, adipose, muscle | blood promoter |
| macrophage | rs1063355 | HLA-DQA1 | 0.29 | 3.0 × 10−18 | NA | WB, skin, muscle | blood promoter. breast/skin DNAase |
| macrophage | rs1351111 | KLRC4-KLRK1 | −0.34 | 4.6 × 10−15 | NA | NA | blood + skin promoter |
| macrophage | rs1351111 | KLRK1 | −0.35 | 1.5 × 10−14 | NA | adipose, fibroblast, muscle | blood + skin promoter |
| macrophage | rs2422631 | SIRPB1 | −0.40 | 2.2 × 10−13 | NA | WB, lung, nerve | blood DNAase |
| macrophage | rs28383372 | HLA-DQA2 | 0.25 | 2.2 × 10−13 | NA | WB, lung, adipose | 5+-tissue promotor |
| macrophage | rs866865 | KCNMA1 | −0.30 | 3.7 × 10−13 | IFN-g, rs752372 | WB, adipose, lung | blood enhancer |
| macrophage | rs2278589 | MARCO | −0.40 | 1.8 × 10−12 | NA | adipose, WB, skin | adipocytes, monocytes |
| macrophage | rs1063347 | HLA-DQB1 | −0.29 | 7.9 × 10−12 | NA | WB, lung, skin | blood promoter + histone marks |
| macrophage | rs634512 | LYZ | −0.27 | 2.2 × 10−11 | LPS24, rs1384 | WB, lung, artery | blood promoter. breast/skin DNAase |
| macrophage | rs4528348 | MS4A14 | 0.26 | 5.4 × 10−11 | LPS24, rs2233253 | adipose, lung, nerve | blood promoter + enhancer liver/lung enhancer + DNAase |
| macrophage | rs2327276 | VNN2 | −0.34 | 7.8 × 10−11 | IFN-g, rs1883613 | adipose, WB, lung | blood + skin promoter |
| endothelial | rs28383362 | HLA-DQA2 | −0.34 | 1.5 × 10−22 | NA | WB, muscle, adipose | blood promoter + enhancer |
| endothelial | rs1884841 | TC2N | −0.23 | 1.0 × 10−12 | NA | nerve, adipose, artery | blood DNAse + enhancer |
| endothelial | rs182366 | B3GALNT2 | 0.26 | 7.0 × 10−12 | NA | nerve, adipose, thyroid | blood promoter, skin DNAase |
| endothelial | rs2744944 | UHRF1BP1 | −0.26 | 8.16 × 10−12 | NA | artery, muscle, fibroblast | blood enhancer |
| endothelial | rs2977786 | DEFB1 | −0.27 | 4.3 × 10−11 | NA | adipose, heart, nerve | 5-+ tissue promotor |
| endothelial | rs61799378 | SLC25A24 | −0.28 | 1.5 × 10−10 | NA | testis, WB, fibroblast | blood promoter |
| endothelial | rs4728142 | IRF5 | −0.28 | 3.2 × 10−10 | NA | WB, artery, thyroid | blood/fat promoter |
| endothelial | rs9270111 | HLA-DRB5 | 0.30 | 6.3 × 10−10 | NA | muscle, WB, adipose | blood cell enhancer |
| endothelial | rs3819715 | HLA-DQB1 | −0.35 | 9.0 × 10−10 | NA | adipose, muscle, skin | blood cell enhancer |
| endothelial | rs3760516 | VAMP2 | −0.33 | 9.6 × 10−10 | NA | nerve, brain, thyroid | blood promoter + enhancer |
| adipocyte | rs28383362 | HLA-DQA2 | 0.26 | 4.2 × 10−13 | NA | WB, muscle, adipose | blood promoter |
| adipocyte | rs2977786 | DEFB1 | 0.27 | 4.6 × 10−11 | NA | adipose, heart, nerve | blood promoter |
| adipocyte | rs1812350 | B3GALNT2 | −0.25 | 6.1 × 10−11 | NA | nerve, adipose, thyroid | blood promoter |
| adipocyte | rs1884841 | TC2N | 0.20 | 6.2 × 10−10 | NA | nerve, adipose, artery | heart/muscle promoter |
The first column, “Cell Type,” lists the cell-type proportion estimate included in the G × cell-proportion interaction model. Macrophage proportion interactions replicated in Fairfax et al., 201540 have proxy SNPs and stimuli condition annotated. The top three eQTL tissues in GTEx are listed on the basis of effect size. The “Regulatory Regions” column lists HaploRegv4 annotations at the lead SNP. All promoters, enhancers, and other regulatory annotation enrichments are derived from HaploRegv4.