Fig. 2: Functional characterization of the rs77704739 recessive association near the PELO gene.

a Colocalization plots from LocusCompare for the rs77704739 variant in adipose subcutaneous tissue. As seen in the plots, the signals from both eQTL data and the recessive T2D association results colocalize. b Violin plot from GTEx showing that the recessive rs77704739 variant significantly modifies the expression of PELO gene in subcutaneous (n = 581 independent samples) and visceral adipose tissue (n = 469 independent samples), skeletal muscle (n = 706 independent samples) and pancreas (n = 305 independent samples). The box plots have lines extending from the boxes (whiskers) indicating variability outside the upper and lower quartiles. GTEx V7 was used for colocalization analyses, whereas GTEx V8 was used to generate the violin plots. c Signal plot for chromosome 5 region surrounding rs77704739. Each point represents a variant, with its p-value from the discovery stage on a −log10 scale in the y axis. The x-axis represents the genomic position (hg19). Three credible set variants are located in open chromatin sites in human pancreatic islets, one of them classified as an active promoter and one highly bounded by pancreatic islet-specific transcription factors, such as PDX1, NKX2.2, NKX6.1, and FOXA2.