Table S6 from Genomic architecture and functional effects of potential human inversion supergenes

Table S6. Potential effects of the 17q21.31 and 8p23.1 inversions and β and γ duplications on gene expression across different tissues from the GTEx project and lymphoblastoid cell lines (LCLs) from the Geuvadis project. Inversion and duplication effects were estimated through cis-expression QTLs (eQTLs) mapping by testing associations between imputed inversion/duplication genotypes and gene expression levels from GTEx and Geuvadis samples. To identify the potential lead variants, joint eQTL mapping was performed with other variants followed by 1000 genotype-phenotype permutations and 5% gene-level FDR correction. Linkage disequilibrium (LD) between inversions/duplications and the rest of the variants is based on imputed genotypes in each dataset and only those associations in which the inversion or duplication is in high LD (r2 ≥ 0.8) with the most significant variants according to permuted P-values are listed here. Inversions or duplications that are lead eQTLs in the joint analysis or in very high LD (r2 ≥ 0.95) with the potential lead eQTL are considered lead variants. GTEx variant IDs were mapped to dbSNP IDs and they are shown when no dbSNP ID was available.