Keratinocyte eQTLs (expression Quantitative Trait Loci)

Cis eQTLs (expression Quantitative Trait Loci) maps are derived from keratinocyte cell lines from N=50 subjects, for which RNA-Seq profiles and genotype data were generated. Cell lines were subjected to 8 different conditions implicated in AD pathogenesis: no stimulation, TNF (10ng/ml), IL-4 (10ng/ml), IL-13 (10ng/ml), IL-17A (10ng/ml), IL-17A+TNF, IFNa (5ng/ml), IFNg (5ng/ml). Gene expression values were first normalized by DESeq2, and PEER was used to account for latent confounding factors. The genotype data was generated by the Illumina Infinium CoreExome array , and imputation was performed using 1000 Genomes Project (GRCh37/hg19) as reference panel. Cis (+/- 1Mb from gene transcription start site) eQTL were mapped using FastQTL v2.0 by fitting a linear regression model (p ∼ g + C) where p is the gene expression vector, g is the genotype vector, and C is a matrix of 10 PEER factors derived from gene expression; eQTLs signal was assessed by the effect size corresponding to the term g.
Column Description
variant - The variant ID (chromosome_position_ref_alt) e.g. chr19_226776_C_T. Based on GRCh38 coordinates and reference genome. The chromosome, position, ref and alt values should exactly match same fields in the summary statistics file, with 'chr' prefix added to the chromosome number.
pvalue - Nominal p-value of association between the variant and the molecular trait.
molecular_trait_id - Ensembl gene ID of the molecular trait.
gene_id - HUGO gene ID of the molecular trait.
beta - Regression coefficient from the linear model.
se - Standard error of the beta.
chromosome - GRCh38 chromosome name of the variant (e.g. 1,2,3 ...,X).
position - GRCh38 position of the variant.
ref - Non-effect allele
alt - Effect allele
rsid - The dbSNP rsid of the variant.