Fig. 6
From: sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression
Example liver-specific eQTL, TNKS-rs9987289, in a TFBS of HNF4A that co-localizes with liver-specific phenotypes. a Effect size and 95% confidence interval of TNKS-rs9987289 across 49 tissues in GTEx. b Allele-specific HNF4A ChIP-seq reads over rs9987289 in the liver (see the “Methods” section, two-sided binomial test P value =8.8×10−5). c Normalized expression levels of TNKS in the liver among individuals with different genotypes at rs9987289. P value =3.4×10−4 from GTEx eQTL analysis. d Schematic illustration of hypothesized mechanism: allele-specific binding of HNF4A at rs9987289 and altered levels of expression of TNKS. e Manhattan plot (LocusZoom v0.4.8) [54] of TNKS expression levels in the liver around rs9987289. f Manhattan plot for LDL GWAS around rs9987289