A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs

This dataset contains the summary statistics from regional association plots from GWAS, and conditional eQTL and pQTL analysis in GTEx data, and functional data as described in <i>Venema et al. 2023 "A cis-regulatory element regulates ERAP2 expression through autoimmune disease risk SNPs </i> <dl>see preprint on <a href="https://www.biorxiv.org/content/10.1101/2023.03.03.530973v1"><i>BioRxiv</i></a>
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This dataverseNL dataset contains additional raw, processed, and metadata (see <a href="https://dataverse.nl/api/access/datafile/382543">readme</a> file and reproducible R notebooks (R script and Image) used for the analysis in the manuscript: <br></br>
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<dt>R scripts (markdown + R image) with <i>step-by-step</i> analyses </dt>
<ul>
<li><dd>Figure_2.rmd (see <a href="https://dataverse.nl/api/access/datafile/382486
">"Figure_2.html"</a>)</dd></li>
<li><dd>Figure_3.rmd (see <a href="https://dataverse.nl/api/access/datafile/382504">"Figure_3.html"</a>)</dd>
</li>
<li><dd>Figure_4.rmd (see <a href="https://dataverse.nl/api/access/datafile/382462">"Figure_4.html"</a>)</dd>
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<li><dd>Cell line authentification (including COSMIC reference genotypes) (see folder <b>Appendix</b> in files)</dd></li></ul>

<dt>Experimental data</dt>
<ul><li><dd>The qPCR (Ct value) data for each experiment are outlined the Supplemental Tables (see <a href="https://dataverse.nl/api/access/datafile/382478">here</a>)</dd></li>
<li><dd>The 4C seq data (FASTA and wig files) for the 3 birdshot LCLs can be found in subdirectory of Figure 4 </dd></li>
<li><dd>Copy-number SNP-array data for CRISPR-edited cell lines (see folder "SNP_array_Data" and an example of THP-1 can be found <a href="https://dataverse.nl/api/access/datafile/382483">here</a>)</dd></li></ul>

<dt>Other data used in the manuscript and R scripts</dt>

<ul><li><dd><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9725108/bin/NIHMS1809843-supplement-TableS4.txt">MPRA of ERAP2 eQTLs</i> </a> as reported by <a href="https://pubmed.ncbi.nlm.nih.gov/35298243/"><i> Abell et al. Science 2022</i> </a></li>

<li><dd><a href="https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-020-00745-3/MediaObjects/41588_2020_745_MOESM3_ESM.xlsx">H3K27ac Chip combined with HiC</i> </a> in primary immune cell subsets generated by <a href="https://pubmed.ncbi.nlm.nih.gov/33349701/"><i> Chandra et al., Nat Genet. 2021</i> </a></li>

<li><dd>Supplemental <a href="https://dataverse.nl/api/access/datafile/382484">data</i> </a> originally generated and provided upon request by <a href="https://pubmed.ncbi.nlm.nih.gov/36819665/"><i> Kerner et al., Cell Genomics 2023</i> </a></li>

<li><dd>Summary statistics of ERAP2 eQTL analysis in <a href="https://console.cloud.google.com/storage/browser/gtex-resources">whole blood</i> </a> generated by <a href="https://www.science.org/doi/10.1126/science.aaz1776"><i> GTEx Consortium </i> </a></li>

<li><dd>Summary statistics of ERAP2 pQTL analysis in <a href="https://app.box.com/s/u3flbp13zjydegrxjb2uepagp1vb6bj2">human plasma</i> </a> generated in the INTERVAL study by <a href="https://pubmed.ncbi.nlm.nih.gov/29875488/"><i> Sun et al Nature 2018 </i> </a></li>

<li><dd>Summary statistics of <i>5q15</i> of GWAS in <a href="https://dataverse.nl/api/access/datafile/382440">Birdshot chorioretinopathy</i> </a> (full GWAS summary stats [>1GB] are available in folder "Figure 2/GWAS_summary_stats") generated by <a href="https://pubmed.ncbi.nlm.nih.gov/24957906/"><i> Kuiper et al Hum Mol Gen 2014</i> </a></li>

<li><dd>Summary statistics of GWAS in <a href="https://www.ibdgenetics.org/uploads/cd-meta.txt.gz">Crohn's Disease</i> </a> generated by <a href="https://www.nature.com/articles/ng.717"><i> Franke et al Nat Genet 2010 </i> </a></li>

<li><dd>Summary statistics of <i>5q15</i> of GWAS in <a href="https://dataverse.nl/api/access/datafile/382488">JIA</i> </a> generated by <a href="https://pubmed.ncbi.nlm.nih.gov/23603761/"><i> Hinks et al Nat Genet 2013 </i> </a></li>

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