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

<b>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.</b> 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 (<i>r</i>² ≥ 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 (<i>r</i>² ≥ 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.

**表S6. 17q21.31与8p23.1倒位、β和γ重复对基因型组织表达（Genotype-Tissue Expression, GTEx）项目不同组织以及Geuvadis项目淋巴母细胞系（lymphoblastoid cell lines, LCLs）中基因表达的潜在影响**
倒位与重复的效应通过顺式表达定量性状位点（cis-expression QTLs，简称eQTLs）定位进行估算，即检验GTEx项目不同组织样本与Geuvadis项目淋巴母细胞系样本中经填充的倒位/重复基因型与基因表达水平之间的关联。为鉴定潜在的先导变异，研究团队联合其他变异开展联合eQTL定位，随后进行1000次基因型-表型置换检验，并实施5%基因水平的错误发现率（False Discovery Rate, FDR）校正。倒位/重复与其余变异之间的连锁不平衡（Linkage Disequilibrium, LD）基于各数据集内的填充基因型计算；本列表仅纳入倒位或重复与根据置换检验P值得到的最显著变异呈高度连锁不平衡（r² ≥ 0.8）的关联结果。在联合分析中作为先导eQTL，或与潜在先导eQTL呈极强连锁不平衡（r² ≥ 0.95）的倒位或重复，将被认定为先导变异。GTEx变异ID已映射至单核苷酸多态性数据库（dbSNP）ID，若无可用的dbSNP ID，则直接展示原GTEx变异ID。