# 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                                                                        |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/coding-variant-associations-format.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.