> 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/proteomics-results.md).

# 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