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Table S4 from Genomic architecture and functional effects of potential human inversion supergenes

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posted on 2022-05-09, 12:35 authored by Elena Campoy, Marta Puig, Illya Yakymenko, Jon Lerga-Jaso, Mario Cáceres
Table S4. Possible functional effects of inversions 17q21.31 and 8p23.1 tag SNPs. Variant Effect Predictor (VEP) was used to annotate 2,568 global tag SNPs (r2 ≥ 0.95) for inversion 17q21.31 and 9 European tag SNPs (r2 ≥ 0.90) for inversion 8p23.1. VEP results were complemented with additional annotations, including phenotypes and Mastermind annotations, Combined Annotation Dependent Depletion (CADD) score, Consensus Deleteriousness (CONDEL) score, LoFtool, MaxEntScan, SpliceAI and BLOSUM62 conservation score. SNP IDs with a different genomic position in VEP analysis were excluded. In 17q21.31 SNPs with three described alleles, only the alleles present in H1 and H2 haplotypes are shown. For inversion 17q21.31, only SNPs affecting coding regions, UTRs, splicing signals, promoters, enhancers, and CTCF and transcription factor binding sites are listed in this table, but all analyzed variants are included for inversion 8p23.1.

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    Philosophical Transactions of the Royal Society B: Biological Sciences

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