# Core analysis results files

FinnGen core analysis results files are available in the Sandbox.

Each core analysis results file is described in the following sections:

* [Genotype cluster plots](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/genotype-cluster-plots-format)
* [GWAS results](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/gwas-results-format)
* [Finemapping](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/finemapping-results-format)
* [Colocalization](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/colocalization-results-format)
* [Autoreporting data](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/autoreporting-results-format)
* [Sex-specific GWAS results](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/sex-specific-gwas-results-format)
* [Recessive GWAS results](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/recessive-gwas-results-format)
* [UKBB - FinnGen meta-analysis](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/ukbb-finngen-meta-analysis-file-formats)
* [Pairwise endpoint genetic correlations](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/pairwise-endpoint-genetic-correlation-format)
* [Heritabilities](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/heritabilities)
* [Coding variant subset](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/coding-variant-associations-format)
* [HLA association results](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/hla-association-results)
* [Proteomics results](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/proteomics-results)
* [Chip EWAS (Exome-Wide Association Scan)](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/chip-gwas)

See [Release Notes](https://docs.finngen.fi/release-notes) to view all data releases to the Sandbox.

**Data freeze/Release specific analysis reports:**

[Analysis report R12](https://www.finngen.fi/system/files/2023-11/finngen_R12_analysis_document_GWAS.pdf)

[Analysis report R11](https://www.finngen.fi/system/files/2023-05/FinnGen_R11_analysis_document_GWAS.pdf)

[Analysis Report R10](https://www.finngen.fi/system/files/2022-11/FinnGen_R10_analysis_document_GWAS.pdf)

[Analysis Report R9](https://www.finngen.fi/en/members/document/302)

[Analysis Report R8](https://www.finngen.fi/en/members/document/270)

[Analysis Report R7](https://www.finngen.fi/en/members/document/255)

[Analysis Report R6](https://www.finngen.fi/en/members/document/176)

[Analysis Report R5](https://www.finngen.fi/en/members/document/175)

### **Example core analysis result files from FinnGen Release 12 (R12)**

**FinnGen DF12** [**sex-specific GWAS**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/sex-specific-gwas-results-format) **and heterogeneity results:**

**Female-/male-specific summary statistics**: gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/sex\_difference/summary\_stats/

**Female-male meta-analysis summary statistics**: gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/sex\_difference/meta\_analysis/meta\_summary\_stats/

**Aggregated meta-analysis results (all endpoints, single-sex assoc P<=5E-8)**: gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/sex\_difference/meta\_analysis/sex\_specific\_meta\_gwsig\_in\_either\_sex\_all\_endpoints.tsv.gz

**FinnGen DF12** [**LOF** ](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/other-analyses-available/lof-burden-test)**results:**

gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/lof/

**FinnGen DF12** [**colocalization**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/colocalization-results-format) **results**\
\&#xNAN;***data:*** gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/colocalization/\
\&#xNAN;***documentation:*** green/finngen\_R12/finngen\_R12\_analysis\_documentation/finngen\_R12\_colocalization.md gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_documentation/finngen\_R12\_colocalization.pdf

**FinnGen DF12** [**PRS** ](https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/genotype-data/types-of-genotype-files-available/prs-data)**results:**\
gs\://finngen-production-library-red/finngen\_R12/prs\_1.0

**FinnGen DF12** [**conditional analysis**](https://docs.finngen.fi/background-reading/conditional-analysis) **and** [**genetic correlation**](https://docs.finngen.fi/background-reading/heritability-and-genetic-correlations) **results:**\
gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/genetic\_correlation/\
gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/conditional\_analysis/

**FinnGen DF12** [**HLA association**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/hla-association-results) **analysis results**

***data:*** gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/hla/

***documentation:***\
gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_documentation/finngen\_R12\_hla\_analysis.md gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_documentation/finngen\_R12\_hla\_analysis.pdf**FinnGen**&#x20;

**R12** [**autoreporting**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/autoreporting-results-format) **&** [**finemapping**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/finemapping-results-format) **results**

* *finemapping data:* /finngen/library-green/finngen\_R12/finngen\_R12\_analysis\_data/finemap
* *autoreporting data:* /finngen/library-green/finngen\_R12/finngen\_R12\_analysis\_data/autoreporting
* *documentation:* /finngen/library-green/finngen\_R12/finngen\_R12\_analysis\_documentation/

**FinnGen R12** [**hla data**](https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/genotype-data/types-of-genotype-files-available/imputed-hla-alleles)

* /finngen/library-red/finngen\_R12/hla\_1.0/

**FinnGen R12 meta-analysis results**

* The data and documentation location in the Sandbox
* [FinnGen + UKBB meta-analysis](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/ukbb-finngen-meta-analysis-file-formats) (856 binary and 10 progression endpoints):
  * gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/meta\_analysis/ukbb/

**FinnGen DF12** [**GWAS  data**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/gwas-results-format)

* data: gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_data/summary\_stats
* documentation: gs\://finngen-production-library-green/finngen\_R12/finngen\_R12\_analysis\_documentation/
* pheweb link: <https://r12.finngen.fi>

**FinnGen DF12 Annotation file**

* Variant annotation file with INFO scores and other annotations `gs://finngen-production-library-green/finngen_R12/finngen_R12_analysis_data/annotations/R12_annotated_variants_v1.gz`

### **Example core analysis result files from FinnGen Release 11 (R11)**

[**FinnGen + UKBB meta-analysis**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/ukbb-finngen-meta-analysis-file-formats) **(762 endpoints) R11:**

* gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/meta\_analysis/ukbb/

**FinnGen Release 11** [**coding variant association results**](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/coding-variant-associations-format) **and documentation**

* The data and documentation location in the Green Library
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/coding/

**FinnGen R11 HLA analysis results.** The data and documentation location in the green library:

* gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/hla/
* gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_documentation/finngen\_R11\_hla\_analysis.md
* gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_documentation/finngen\_R11\_hla\_analysis.pdf

**FinnGen Release 11 heritability and genetic correlation analysis outputs**

* The data and documentation location in the green library:
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/ldsc/

**FinnGen Release 11 GWAS, finemapping, conditional analysis, colocalization and autoreporting data.** The data and documentation location in the green library:

* GWAS:
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/summary\_stats
* Fine-mapping:
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/finemap
* Conditional analysis:
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/conditional\_analysis
* Autoreporting:
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/autoreporting
* Colocalization:
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_data/colocalization
* Documentation available at:
  * gs\://finngen-production-library-green/finngen\_R11/finngen\_R11\_analysis\_documentation/
  *
* Finngen R11 [cluster plot data](https://github.com/finngen-user-documentation/Draft_of_FG_Analyst_Handbook/blob/master/finngen-data-specifics/green-library-data-aggregate-data/core-analysis-results-files/broken-reference/README.md). These data files contain genotype intensities per variant for a subset of samples that are used in cluster plots (released in the green library).
  * Data and documentation location in Sandbox:
    * `/finngen/library-red/finngen_R11/cluster_plot_1.0`
  * Detailed paths to library red data from manifest:
    * `/finngen/library-red/finngen_R11/cluster_plot_1.0/manifest.txt`
* Colocalization between pQTLs and all genome wide significant hits in R10 .
  * Data location in the green library:
    * `gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/`
  * The results are browsable in FinnGen browser (e.g. <https://results.finngen.fi/region/H7_AMD/1:196510779-196910779>, scroll down for colocalization table)

**pQTL analysis and finemapping results**

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

###

### **Example core analysis result files from FinnGen Release 10 (R10)**

**Colocalization between pQTLs and all genome wide significant hits in R10**

`gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/`

* pQTL analysis and finemapping results
  * 828 and 619 samples from SomaLogic and Olink respectively samples
  * Data location in the green library:
    * `gs://finngen-production-library-green/omics/proteomics/release_2023_03_02/`
* Colocalization between pQTLs and all genome wide significant hits in R10 .
  * Data location in the green library:
    * `gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/`
  * The results are browsable in FinnGen browser (e.g. <https://results.finngen.fi/region/H7_AMD/1:196510779-196910779>, scroll down for colocalization table)
* Heritabilities and genetic correlations: `/finngen/library-green/finngen_R10/finngen_R10_analysis_data/ldsc/`
* Imputed HLA allele genotypes `/finngen/library-red/finngen_R10/hla_1`
* GWAS data location:
  * `/finngen/library-green/finngen_R10/finngen_R10_analysis_data/summary_stats`
  * Sex-specific association analysis results (under summary\_stats)
  * Variant annotation file with INFO scores and other annotations `/finngen/library-green/finngen_R10/finngen_R10_analysis_data/annotations/`
* Fine-mapping data location:
  * `/finngen/library-green/finngen_R10/finngen_R10_analysis_data/finemap`
* Conditional analysis data location:
  * `g/finngen/library-green/finngen_R10/finngen_R10_analysis_data/conditional_analysis`
* Autoreporting data location:
  * `/finngen/library-green/finngen_R10/finngen_R10_analysis_data/autoreporting`
* Colocalization data location:
  * `/finngen/library-green/finngen_R10/finngen_R10_analysis_data/colocalization`
* Documentation location:
  * `/finngen/library-green/finngen_R10/finngen_R10_analysis_documentation/`
* FinnGen 10 HLA allele analysis results: `/finngen/library-green/finngen_R10/finngen_R10_analysis_data/hla/`
  * Documentation available at:
    * `/finngen/library-green/finngen_R10/finngen_R10_analysis_documentation/finngen_R10_hla_analysis.pdf`
* Finngen R10 cluster plot data:`/finngen/library-green/finngen_R10/cluster_plots/`
  * The cluster plot tsv files, that contain genotype intensities per variant for a subset of samples used in the cluster plots are released to the Sandbox at:

    `/finngen/library-red/finngen_R10/cluster_plot_1.0/data/`

    * Detailed paths of this data from the manifest file: `/finngen/library-red/finngen_R10/cluster_plot_1.0/manifest.txt`
* FinnGen R10 PRS data (version 1.0): `/finngen/library-red/finngen_R10/prs_1.0/`

**Example core analysis result files from FinnGen Release 8 (R8)**

* **Genotype cluster plot file**: `/finngen/library-red/finngen_R8/cluster_plot_1.0/`
* **GWAS results**: `/finngen/library-green/finngen_R8/finngen_R8_analysis_data/summary_stats/`
* **Finemapping results**: `/finngen/library-green/finngen_R8/finngen_R8_analysis_data/finemap/`
* **Colocalization results**: `/finngen/library-green/finngen_R8/finngen_R8_analysis_data/colocalization/`
* **Autoreporting results**: `/finngen/library-green/finngen_R8/finngen_R8_analysis_data/autoreporting/`
* **UKBB-FinnGen meta-analysis results**: `/finngen/library-green/finngen_R8/finngen_R8_analysis_data/ukbb_meta/`
* **All heritability estimates and genetic correlations calculated by ldsc software**: `/finngen/library-green/finngen_R8_analysis_data/ldsc/`
* **Pairwise endpoint genetic correlation format**: `/finngen/library-green/finngen_R8_analysis_data/ldsc/finngen_R8_FIN.ldsc.summary.tsv`
* **Heritabilities:** `/finngen/library-green/finngen_R8_analysis_data/ldsc/finngen_R8_FIN.ldsc.heritability.tsv`
* **Coding variant subset format**:`/finngen/library-green/finngen_R8/finngen_R8_analysis_data/summary_stats/coding_variants/coding_variants.tsv.gz` (all binary endpoints)
* **All quantitative traits** (coding variant subset): `/finngen/library-green/finngen_R8/finngen_R8_analysis_data/summary_stats/coding_variants/coding_variants.quantitative.tsv.gz`
* **Chip GWAS** (will be released for DF9, previously was released for DF5)
* **Annotation file** (file including eg. counts of each variant per batch and most\_severe\_consequence and gene; used by finemapping pipeline and Regenie): `/finngen/library-green/finngen_R8_analysis_data/annotations/`
* **Mapping for imputed variants**: `/finngen/library-green/finngen_R8_analysis_data/variant_mapping/finngen.variants.tsv`
* **Full dbsnp**`: /finngen/library-green/finngen_R8_analysis_data/variant_mapping/rsid_map.tsv`
* **Phenotype case/control N**: `finngen/library-green/finngen_R8/finngen_R8_pheno.tsv`
* **Release documentation**: `/finngen/library-green/finngen_R8/finngen_R8_analysis_documentation/`

All `green-library` files can also be seen outside of the Sandbox, without red-data access, by using [google cloud console](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/how-can-you-download-green-data). See instructions from [here](https://docs.finngen.fi/finngen-data-specifics/green-library-data-aggregate-data/how-can-you-download-green-data). When using google cloud console `finngen/library-green/` within the above paths is replaced by`production-library-green`, otherwise the paths are the same.