> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/coding-variant-associations-format.md).

# Coding variant associations format

Coding variant association analysis results for [imputed data](/finngen-data-specifics/red-library-data-individual-level-data/genotype-data/imputation-panel.md) aggregated across all phenotypes.

**Files:**

`coding_variants.tsv.gz:` binary endpoints

`coding_variants.quantitative.tsv.gz:` quantitative phenotypes

Files are compressed tabix-indexed files containing all coding variants across all [regenie](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-regenie.md)-analysed phenotypes with following conditions:

1. [P-value](/background-reading/p-values.md) < 1e-4
2. Variant is categorized as one of the following:

* transcript\_ablation
* splice\_donor\_variant
* stop\_gained
* splice\_acceptor\_variant
* frameshift\_variant
* stop\_lost
* start\_lost
* inframe\_insertion
* inframe\_deletion
* missense\_variant
* protein\_altering\_variant

**File columns:**

| **Column name**    | **Description**                                                                               |
| ------------------ | --------------------------------------------------------------------------------------------- |
| <p>#chrom<br></p>  | <p>Chromosome<br></p>                                                                         |
| pos                | Position                                                                                      |
| ref                | Reference allele                                                                              |
| alt                | Alternative allele                                                                            |
| pval               | P-value                                                                                       |
| mlogp              | #NAME?                                                                                        |
| beta               | Beta                                                                                          |
| sebeta             | Standard error                                                                                |
| af\_alt            | Alternative allele frequency                                                                  |
| af\_alt\_cases     | Alternative allele frequency in cases (non-quantitative only)                                 |
| af\_alt\_controls  | Alternative allele frequency in controls (non-quantitative only)                              |
| fin.AF             | Alternative allele frequency in the Finnish population (GnomAD)                               |
| nfsee.AF           | Alternative allele frequency in the non-Finnish-Swedish-Estonian European population (GnomAD) |
| rsid               | rsID                                                                                          |
| gene\_most\_severe | Nearest gene                                                                                  |
| most\_severe       | Variant type                                                                                  |
| fin.enrichment     | Finnish enrichment (fin.AF / nfsee.AF)                                                        |
| phenotype          | Phenotype abbreviation                                                                        |