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Chronic kidney disease (CKD) region on chr18 (chr18:13.9–19.1 Mb).

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posted on 2023-01-24, 18:34 authored by Frode Lingaas, Katarina Tengvall, Johan Høgset Jansen, Lena Pelander, Maria H. Hurst, Theo Meuwissen, Åsa Karlsson, Jennifer R. S. Meadows, Elisabeth Sundström, Stein Istre Thoresen, Ellen Frøysadal Arnet, Ole Albert Guttersrud, Marcin Kierczak, Marjo K. Hytönen, Hannes Lohi, Åke Hedhammar, Kerstin Lindblad-Toh, Chao Wang

(A) Eighteen Bayesian candidate markers (green dots) were observed in this region, and are present in two linkage disequilibrium (LD) blocks. (B) Annotated genes were identified around the CKD region. One selection signal of dog domestication and a ~500 Kb reported genomic duplicates were observed in this region. 2,064 imputed variants were found within the same LD of Bayesian candidate markers. (C) 76 imputed SNPs with phyloP score > 1 were lifted to human genome (hg38), and intersected with the regulatory elements from the candidate cis-Regulatory Elements (cCRE; red bars) and GeneHancer databases (blue bars), as well as the hypersensitivity (HS) signal from 95 cell lines (the height of the bar indicated the number of cell lines with the HS signal). (D) Eight putative regulatory SNPs (C3-C10) from the CKD region were tested with electrophoretic mobility shift assays (EMSAs). SNPs C8 and C9 showed alternative binding ability between the risk and protective alleles in HEK293 cell line.