# Proteomics results

## **Data locations in the green library:**

* `gs://finngen-production-library-green/omics/proteomics/release_2023_10_11/`
* `gs://finngen-production-library-green/omics/proteomics/release_2023_03_02/`

**Colocalization between pQTLs and all genome wide significant hits in releases:**

* Data location in the green library:
  * `gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/colocalization/`
  * `gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/colocalization/`
  * `gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/`
* The results are browsable in FinnGen browser (e.g. for a region <https://results.finngen.fi/region/H7_AMD/1:196510779-196910779> \[scroll down for colocalization table] or for a gene <https://results.finngen.fi/gene/PCSK9> \[scroll down for pqtls and colocs])

## General description

Compiled summary stats and fine-mapping results for proteomics QTL (See below for data locations) in imputed SNPs on FINNGEN. Two platforms are included, **Olink** and **SomaScan**. The association results are from **PLINK2** and in unrelated samples only. Due to different sample sizes, the SNP sets are not the same between those two datasets.

## Data

#### Results from Somascan and Olink are in their own subdirectories in common format as below.

<figure><img src="/files/R7K7Zb3mbeEX0LxR1Muh" alt=""><figcaption></figcaption></figure>

### Column descriptions for pQTL results

* **CHR:** chromosome for variants
* **POS**: BP of the variant
* **ID:** SNP name (CHR\_POS\_REF\_ALT)
* **REF:** reference allele provided in FINNGEN imputed data
* **ALT:** alternative allele, this is the effect allele (aka. A1, effect allele, A0 in some software)
* **ALT\_FREQ:** allele frequency of the alternative allele
* **BETA:** effect size in additive model
* **SE:** standard error of the effect size T\_STAT: t statistics from PLINK2
* **P:** p-value in association test N: per- SNP sample size for the SNP

### Map the probes's name to gene symbol

**File: probe\_map.tsv**

* **Olink**: geneName is the gene symbol which is also the probe name in Olink, other columns are chr (chromosome), start and end of the gene from Gencode V43
* **Somascan**: AptName is the probe name in Somascan, other columns are geneName (gene symbol), start and end of the gene from Gencode V43

## software

* **Assocation:** PLINK2 v2.00a3.3LM AVX2 Intel (3 Jun 2022)
* **Finemap:** FINNGEN/finemapping-pipeline, revised on R10, hash e0792ea
* **Autoreporting:** FINNGEN/autoreporting, revised on hash 9dbea66


---

# 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/proteomics-results.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.