Data access

FTP downloads

On our FTP site you will find both tab-delimited flat files as well as parquet files.

The metadata for all uniformly processed datasets can be found here: release 7, pre-release 8.

The URLs of all individual tab-delimited files together with metadata can be found here.

All file formats are explained here.

Fine-mapped credible sets

Fine mapping results for individual datasets can be downloaded from here: release 7, pre-release 8.

Merged credible set files for all quantification methods can be downloaded from here: pre-release 8.

Tabix

Instead of downloading the full tab-delimited files from the FTP, you can also use tabix to access specific regions from those files. For example, to fetch the association between rs4239702 variant and all genes in the +/- 1Mb window in the monocyte samples from the BLUEPRINT study (QTD000021), you can use the following command:

tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/QTS000002/QTD000021/QTD000021.all.tsv.gz 20:46120612-46120613

You can also use curl to access column names:

curl -s ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/QTS000002/QTD000021/QTD000021.all.tsv.gz | zcat | head -n 1

However, please note that frequent tabix requests to the FTP server are sometimes interpreted as denial-of-service (DoS) attacks by the EBI firewall. This can result in your IP address being blacklisted which then needs to be manually whitelisted again. The root cause is that both tabix requests and DoS attacks on the FTP manifest as frequent incomplete file download attempts in a short period of time. We thus recommend limiting the frequency of tabix requests (e.g. one request in every couple of seconds) or downloading the full summary statistics files if many requests need to be made.

RESTful API

The RESTful API has now been deprecated and is no longer available.

ELIXIR-Estonia credible set browser

ELIXIR-Estonia has developed an interactive credible set browser, where you can quickly check if your variant of interest is likely to be a causal eQTL variant.

Examples

• Inflammatory bowel disease lead variant at the PDGFB locus: rs2413583

Complete fine mapping results can be downloaded from our FTP.

Tutorials

• Using tabix in R to fetch summary statistics and perform colocalisation

Frequently Asked Questions (FAQ)

Which allele is the effect allele?

The ALT allele is always the effect allele. See here for the full description of the summary statistics data fields.

How are multiple rsids handled?

We store one rsid per line in our summary staistics files. Thus, if a single variant maps to multiple rsids in dbSNP v151, then summary statistics from this variant will be duplicated over multiple rows. This simplifies querying by rsid, but we recommend removing duplicate entires before any downstream analysis (e.g. colocalisation) as is done in this tutorial.

How are multi-allelic variants handled?

Multi-allelic variants are included in the analysis, but they are split over multiple and have unique ALT alleles and variant IDs (but might have the same rsids).

Do you also map QTLs on the X chromsome?

X chromosome QTLs were added in release 5. List of studies with X chromosome QTLs can be found here.

Can you provide access to additional data not described on this page?

We often get requests to access additional data that are not available from our FTP server or the credible set browser. Most commonly, these involve full nominal summary statistics for all tested exons or leafcutter junctions in a subset of eQTL Catalogue tissues or datasets. Unfortunately, we do not store these results long term due to space constraints, and we are thus unable to respond to such individual ad hoc requests.