eRNA_QTL_website.pptx

X
Web portal for eRNA-QTLs
A step-by-step guide
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.
Part 1: Querying eRNA-QTLs of interest
Part 2: Genome Browser
Part 3: Visualization of GWAS and eRNA-QTLs
colocalization events
Part 4: Disease/trait-associated eRNA-QTLs
Part 5: Downloading data of eRNA-QTLs
Step 2:
Select tissue type of interest (e.g.
Adipose_Subcutaneous)
Part 1 Querying eRNA-QTLs of interest
Step 1: Quick search by eRNA or rs ID (e.g.
ENSR00000069687 or rs4467826)
Step 3:
Search a rsid ( e.g.
rs9323457)
Step 4:
Relevant eRNA-QTLs will
automatically show
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.
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).
Mouse click to see
detailed information
Mouse click to config tracks
Part 2 Genome Browser
Part 3 Visualization of GWAS and eRNA-QTLs
colocalization events
Step 1: Click to load
example data
Quick guide
Part 3 Visualization of GWAS and eRNA-QTLs
colocalization events
Step 2: Click to plot
Step 3: Download
PDF file
Part 4: Disease/trait-associated eRNA-QTLs
Step 1:Search a disease/trait
type (e.g. Telomere length)
Step 2:
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.
Part 5 Downloading data of eRNA
QTLs Step 1: Click
“Downloads” h
Step 2:
Click any file name for Visualizing
and Downloading
Download file:
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eRNA_QTL_website.pptx

  • 1. Web portal for eRNA-QTLs A step-by-step guide
  • 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: Disease/trait-associated eRNA-QTLs Part 5: 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 eRNA or rs ID (e.g. ENSR00000069687 or rs4467826)
  • 5. Step 3: Search a rsid ( e.g. rs9323457)
  • 6. Step 4: Relevant eRNA-QTLs will automatically show
  • 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 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
  • 12. Part 4: Disease/trait-associated eRNA-QTLs Step 1:Search a disease/trait type (e.g. Telomere length) Step 2: 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.
  • 13. Part 5 Downloading data of eRNA QTLs Step 1: Click “Downloads” h
  • 14. Step 2: Click any file name for Visualizing and Downloading Download file: