> 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/red-library-data-individual-level-data.md).

# Red Library Data (individual level data)

## Types of red data available in FinnGen

Clinical codes are recorded in nationwide registries which are harmonized together into one table in FinnGen

<figure><img src="/files/-MhYMcBcgsEE78N8quSw" alt=""><figcaption></figcaption></figure>

### Code sets in detailed longitudinal data

* **Kela (Social insurance institution)**
  * The REIMB/KELA codes are unique to Finland - these are longterm reimbursement codes for a class of drugs and imply a robust review of diagnosis. For example, KELA code 307 provides reimbursement for donepezil, galantamine, memantine and rivastigmine and is granted only after review of physician
    * ATC – drug identifiers
    * REIMB – drug reimbursements
    * VNRO – drug product number including dosage and number in package
* **Hilmo/Hospital codes**
  * Diagnosis in ICD-10, ICD-9 and ICD-8
  * Procedures (Nomesco, Finnish Hospital league\*, Heart patient\*\*)
* **Cancer registry**
  * ICD-O-3 (topology, morphology, behavior codes, OBS. no specific information on gradus or metastatic spread)
* **Avohilmo**
  * Diagnosis in ICD-10 and nurse codes ICPC2
  * Procedures (SPAT, Nomesco)
  * Dental codes

\*) Finnish specific procedure codes, \*\*) Finnish specific demanding heart patient procedure code

<figure><img src="/files/qNGxxUz2Fh2ujxHEn9ds" alt=""><figcaption><p>Code sets in detailed longitudinal data</p></figcaption></figure>

### Additional registries

* **Vaccination registry** from primary health care (vaccination, type of vaccination, disease, method and site, approx. date, contains also COVID vaccination)
* **Kidney registry** (only dialysis/transplantation patients, set of diagnosis codes)
* **Digital and population data services agency, birth registry** (reproductive history data - detailed information on births in FinnGen participants)
* **Visual impairment registry** (data on legally blind patients: diagnosis, visual acuity, diameter of visual field, homonyme hemianopsia)
* **Cancer screening registries** (cervical and breast)
* **Parental causes of death** (ICD-8/9/10)
* **Infectious diseases** (COVID positive patients and their treatment)
* **Congenital malformations** (congenital chromosomal and structural anomalies, congenital hypothyroidism, teratomas)
* **Service sector data** (service sector (e.g. elderly home), contact type, specialty, hospital type, urgency, professional type, Kela drug reimbursement costs, Kela drug reimbursement category)

### Minimum phenotype data (comes with the samples from the biobanks)

* Age
* smoking status (yes/no, current/former/never, current/occasional/quitter/former/never)
* BMI

## Genetic data (germline)

* GWAS array genotypes (500,000)
  * 420,000 samples genotyped with ThermoFisher Axiom custom arrays (v1 and V2). The following numbers are from v2:
    * Total of 664,510 markers including:
      * About 500,000 core GWAS markers
      * 116,000 coding variants enriched in Finland
      * \>10,000 specific markers for the HLA/KIR region
      * about 15,000 ClinVar variants
      * about 4,600 pharmacogenomic variants
      * 57,000 selected markers of special interest for partners
  * 70-80,000 samples genotypes with various other GWAS arrays (Legacy genotypes)
* Imputed genotypes (520,000)
  * \~21,3M variants per individual
  * imputed using Finnish specific WGS reference panel of \~9000 individuals

**In this section we will share the following:**

[Genotype data](/finngen-data-specifics/red-library-data-individual-level-data/genotype-data.md)

[Phenotype data](/finngen-data-specifics/red-library-data-individual-level-data/what-phenotype-files-are-available-in-sandbox-1.md)

[Expansion Area 3 (EA3) studies](/finngen-data-specifics/expansion-area-3-ea3-projects.md)