Data access

FTP downloads

On our FTP site you will find both tab-delimited flat files as well as HDF5 files.

The metadata for all uniformly processed datasets can be found here.

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

Fine mapping results can be downloaded from here.

QTL coverage plots can be downloaded from here here

All file formats are explained here.

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

You can query eQTL summary statistics datasets using our RESTful API. See documentation and a tutorial for more details.

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

• Fetching summary statistics and performing colocalisation with eQTL Catalogue API v2
• 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.