Phenotype data

FinnGen phenotype data is available to Sandbox users.

Sandbox directory

Phenotype data is available in the following sandbox directory:

/finngen/library-red/finngen_R[RELEASE]

For example, FinnGen Data Release 12 files are in the following directory:

• Release 12: /finngen/library-red/finngen_R12/

Registers

FinnGen contains phenotype data from the following registers:

Abbreviation *1	Abbreviation *1	Register	Source
PURCH	LAAKE_ATC	Kela drug purchase register (since 1995)	Social Insurance Institution of Finland (Kela)
REIMB	KELAEK	Kela drug reimbursement register (since 1964)	Social Insurance Institution of Finland (Kela)
INPAT	HILMO	Inpatient Hilmo register (Health-Hilmo) (since 1969)	Finnish Institute for Health and Welfare (THL) Care Register for Health Care
OPER_IN	OPER	Inpatient Hilmo register (Health-Hilmo) operations (since 1969)	Finnish Institute for Health and Welfare (THL) Care Register for Health Care
OUTPAT	ERIK_AVO	Specialist outpatient Hilmo register (Health-Hilmo) (since 1998)	Finnish Institute for Health and Welfare (THL) Care Register for Health Care
OPER_OUT	ERIK_OPER	Specialist outpatient Hilmo register (Health-Hilmo) operations (since 1998)	Finnish Institute for Health and Welfare (THL) Care Register for Health Care
PRIM_OUT	AVO	Primary health care outpatient visits register (Avohilmo) (since 2011)	Finnish Institute for Health and Welfare (THL) Register of Primary Heath Care visits
CANC	CANCER	Cancer register (since 1953)	Finnish Cancer Registry
DEATH	DEATH	Cause of death register (since 1969)	Statistics Finland

*1 Different abbreviations may be used in different contexts. For example, the detailed longitudinal data file uses the abbreviations in the first column and endpoint longitudinal data uses the abbreviations in the second column.

Further information

The phenotype data files are described in the following sections:

• Register data
• Detailed longitudinal data
• Endpoint and endpoint longitudinal data
• Kanta Lab data
• Minimum extended phenotype data
• Minimum longitudinal data
• Other registry data files in Sandbox

A list of variables received from the registers through THL and other information about the registers is available in the FinnGen members area here. Some additional information about the variables is available here.

The FinnGen register data was presented in the FinnGen data users meeting on 12 January 2021.