> For the complete documentation index, see [llms.txt](https://finngen.gitbook.io/documentation/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://finngen.gitbook.io/documentation/r2/data-download.md).

# Data download

To download FinnGen summary statistics you will need to fill the online form at [this link](https://elomake.helsinki.fi/lomakkeet/124935/lomake.html). You will then receive an email containing the detailed instructions for downloading the data.

## Using FinnGen data for publications

Please remember to **acknowledge** the FinnGen study when using these results in publications. 

You can use the following text: 

> *We want to acknowledge the participants and investigators of FinnGen study*.

## Manifest

The Manifest file with the link to all the downloadable summary statistics is available at: <https://storage.googleapis.com/finngen-public-data-r2/summary_stats/r2_manifest.tsv>

## Description

GWAS summary stats (tab-delimited, bgzipped, genome build 38, filtered to INFO > 0.6, [tabix](https://github.com/samtools/htslib) index files included) are named as `{endpoint}.gz`. For example, endpoint `I9_CHD` has `I9_CHD.gz`  and `I9_CHD.gz.tbi`.

To learn more about the methods used, see section [GWAS](/documentation/r2/methods/phewas.md). &#x20;

The `{endpoint}.gz` have the following structure:

| Column name     | Description                                                                                          |
| --------------- | ---------------------------------------------------------------------------------------------------- |
| `chrom`         | chromosome on build GRCh38 (`1-22, X`)                                                               |
| `pos`           | position in base pairs on build GRCh38                                                               |
| `ref`           | reference allele                                                                                     |
| `alt`           | alternative allele (effect allele)                                                                   |
| `rsids`         | variant identifier                                                                                   |
| `nearest_genes` | nearest gene name from variant                                                                       |
| `pval`          | p-value from [SAIGE](https://github.com/weizhouUMICH/SAIGE)                                          |
| `beta`          | effect size estimated with [SAIGE](https://github.com/weizhouUMICH/SAIGE) for the alternative allele |
| `sebeta`        | standard deviation of effect size estimated with [SAIGE](https://github.com/weizhouUMICH/SAIGE)      |
| `maf`           | minor allele frequency                                                                               |
| `maf_cases`     | minor allele frequency among cases                                                                   |
| `maf_controls`  | minor allele frequency among controls                                                                |