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Table 3.xls (9.5 kB)

Results of Simple Sum colocalization and contrasting colocalization analyses for the three meconium ileus genome-wide significant loci, and colocalization posterior probabilities from COLOC and eCAVIAR.

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posted on 2019-02-26, 18:37 authored by Jiafen Gong, Fan Wang, Bowei Xiao, Naim Panjwani, Fan Lin, Katherine Keenan, Julie Avolio, Mohsen Esmaeili, Lin Zhang, Gengming He, David Soave, Scott Mastromatteo, Zeynep Baskurt, Sangook Kim, Wanda K. O’Neal, Deepika Polineni, Scott M. Blackman, Harriet Corvol, Garry R. Cutting, Mitchell Drumm, Michael R. Knowles, Johanna M. Rommens, Lei Sun, Lisa J. Strug

The eQTL evidence is the GTEx p-value based on the -log10(eQTL p) scale for a specified gene and tissue. The meconium ileus-SNP association evidence is the -distributed Wald test statistic obtained in this study. Analytical (and permutation-based) Simple Sum (SS) colocalization p-values correspond to each individual tissue and evaluates if the eQTLs and meconium ileus-associated variants colocalize. Simple Sum contrasting (SSC) colocalization p-value evaluates if the eQTLs in the pancreas colocalize with meconium ileus-associated variants more than eQTLs in another tissue; NAs are listed for the pancreas since we do not contrast pancreas with itself. All p-values are one-sided because only positive association implies eQTL-association colocalization (i.e. eQTL peaks coincide with association peaks). COLOC [43] PP represents the posterior probability of eQTL-association colocalization calculated for each individual tissue. eCAVIAR [44] calculates SNP-level colocalization posterior probability (CLPP) for each variant in a locus for a given gene and in a given tissue. The regional colocalization probability (RCP) can be defined by summation of the SNP-level CLPP in a given LD block; RCP is recommended in [49] and the results are provided in the ‘eCAVIAR RCP’ column. eCAVIAR maximum regional CLPP provides similar qualitative results as eCAVIAR RCP thus are not shown here.