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
• 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
Part 4: Disease/trait-associated eRNA-QTLs
Part 5: Downloading data of eRNA-QTLs
4. Step 2:
Select tissue type of interest (e.g.
Part 1 Querying eRNA-QTLs of interest
Step 1: Quick search by eRNA or rs ID (e.g.
ENSR00000069687 or rs4467826)
7. Part 2 Genome Browser
Step 1: Click “Genome Browser” in navigation bar.
This process might consume some time to
load the frame. Thank you for waiting.
8. IGV.js was used to construct the frame of genome browser
Based on the hg38 genome
Search by genome position (e.g.
9. Mouse click to see
Mouse click to config tracks
Part 2 Genome Browser
10. Part 3 Visualization of GWAS and eRNA-QTLs
Step 1: Click to load
11. Part 3 Visualization of GWAS and eRNA-QTLs
Step 2: Click to plot
Step 3: Download
12. Part 4: Disease/trait-associated eRNA-QTLs
Step 1:Search a disease/trait
type (e.g. Telomere length)
Select a tissue(e.g. Adipose Subcutaneous)
This process might consume some time to search the data or scroll
to the next page due to the large data. Thank you for waiting.