2. Data and methods
• Data were obtained from the Genotype-Tissue Expression (GTEx),
including 838 donors, 54 tissues, and two cell lines. Genotype data from
whole-genome sequencing (WGS) was sequenced on an Illumina HiSeq
2000.
• To test for eRNA-QTLs, we first used the permutation pass with 1000
permutations recommended to characterize the null distribution of
associations for each eRNA separately and obtained a 5% false
discovery rate for multiple testing applied in R using qvalue. Second, a
nominal pass was performed. Nominal p-values for all SNP-eRNA pairs
within the cis-window (1Mbp) were obtained with the nominal pass
implemented in the QTLtools package. Both permutation and nominal
pass were applied the QTLtools-implemented “--normal” option to rank
normal transform the phenotype quantifications. SNP-eRNA associations
reaching the significance threshold corresponding to FDR < 0.05 were
retained to further analysis. The eRNA expression matrix was also
normalized using the “--normal” option. Linear regression analysis was
performed between SNPs and all eRNAs outside their cis windows
(1Mbp), accounting for the covariates previously mentioned.
3. Part 1: Querying eRNA-QTLs of interest
Part 2: Genome Browser
Part 3: Visualization of GWAS and eRNA-QTLs
colocalization events
Part 4: Downloading data of eRNA-QTLs
4. Step 2:
Select tissue type of interest (e.g.
Adipose_Subcutaneous)
Part 1 Querying eRNA-QTLs of interest
Step 1: Quick search by gene symbol or rs ID
(e.g. ENSR00000069687 or rs4467826)
7. Part 2 Genome Browser
Step 1: Click “Genome Browser” in navigation bar.
8. IGV.js was used to construct the frame of genome browser
Based on the hg38 genome
Download SVG
Search by genome position (e.g.
chr14:64423444-65063275).
9. Mouse click to see
detailed information
Mouse click to config tracks
Part 2 Genome Browser
10. Part 3 Visualization of GWAS and eRNA-QTLs
colocalization events
Step 1: Click to load
example data
Quick guide
11. Part 3 Visualization of GWAS and eRNA-QTLs
colocalization events
Step 2: Click to plot
Step 3: Download
PDF file
