Benign neoplasm: Extrahepatic bile ducts

CD2_BENIGN_EXTRAHEPATIC_BILE

common bile duct neoplasm: Tumor or cancer of the common bile duct including the ampulla of vater and the sphincter of oddi.

Suggest a new description

Endpoint definition

↥

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D13.5& Hospital discharge: ICD-8 — 2115[1-2] Cause of death: ICD-10 — D13.5& Cause of death: ICD-8 — 2115[1-2] 2 out of 7 registries used, show all original rules.	98
4. Check minimum number of events None	98
5. Include endpoints None	98
6. Filter based on genotype QC (FinnGen only)	98

Control definitions (FinnGen only)

Controls for this endpoint are individuals that are not cases.

Extra metadata

Level in the ICD hierarchy: 4
First used in FinnGen datafreeze: DF2
Parent code in ICD-10: D13
Name in latin: Neoplasma benignum ductuum biliarium extrahepaticorum

NAME	CD2_BENIGN_EXTRAHEPATIC_BILE
CONTROL_EXCLUDE
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D135
HD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_8	2115[1-2]
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	D135
COD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
COD_ICD_8	2115[1-2]
COD_ICD_10_EXCL
COD_ICD_9_EXCL
COD_ICD_8_EXCL
OPER_NOM
OPER_HL
OPER_HP1
OPER_HP2
KELA_REIMB
KELA_REIMB_ICD
KELA_ATC_NEEDOTHER
KELA_ATC
KELA_VNRO_NEEDOTHER
KELA_VNRO
CANC_TOPO
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Similar endpoints

↥

List of similar endpoints to Benign neoplasm: Extrahepatic bile ducts based on the number of shared cases.

Similar with more cases:

Similar with less cases:

Benign neoplasm: Extrahepatic bile ducts

Case counts by codes

↥

FinnGen case counts by registry codes:

Upset plot

Full data table

Summary Statistics

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-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	741	435	299
Only index persons	639	388	251
Unadjusted period prevalence (%)
Whole population	0.01	0.01	0.01
Only index persons	0.01	0.01	0.01
Median age at first event (years)
Whole population	60.15	58.14	63.18
Only index persons	59.14	57.39	61.84

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	98	54	44
Unadjusted period prevalence (%)	0.02	0.02	0.02
Median age at first event (years)	59.65	54.98	65.39

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

No data

CodeWAS (R11)

↥

CodeWAS is a tool for exploring the associations between an endpoint and all of the medical codes and drug codes.

This is a new tool, please reach out using the contact form for feedback and improvement ideas.

First, a cohort is built by matching controls to the endpoint cases using year of birth and sex. Then, a Fisher test is done for all the medical codes and drug codes between the cases and controls of this cohort. Codes are reported in the table below if they have −log₁₀(p-value) ≥ 6.

Matched cohort

Matched cases
90: Matched controls
899

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

D13.5

ICD-10 Finland

Benign neoplasm: Extrahepatic bile ducts

+∞

116.9

JKA21

NOMESCO Finland

Laparoscopic cholecystectomy

13.9

22.3

UJK02

NOMESCO Finland

ERCP

54.6

12.3

D37.6

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Liver, gallbladder and bile ducts

32.7

11.1

JJ1CE

NOMESCO Finland

Liver, bile duct and pancreas endoscopic ultrasound examination

49.4

7.9

JKE98

NOMESCO Finland

Other transduodenal endoscopic operation on bile duct or ampulla of Vater

27.8

7.8

JL5SB

NOMESCO Finland

Endoscopic retrograd cholangiopancreaticography

87.0

7.5

JN1CG

NOMESCO Finland

Extensive MRI examination of upper part of abdomen with high intensity magnet

17.6

7.4

K80.2

ICD-10 Finland

Calculus of gallbladder without cholecystitis

5.3

7.1

D37.7

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Other digestive organs

15.8

6.6

JL5BG

NOMESCO Finland

MRI examinaiton of bile and pancreas ducts with high intesity magnet

19.7

6.4

LabWAS

↥

(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3003785) Carcinoembryonic Ag [Mass/volume] in Serum or Plasma

4.16

9.05

2.3

4.7

2.8

11.7

ug/l

1.19

(3002256) Pathology report gross observation

3.29

5.43

1.3

1.2

—

(3001079) Blood group antibody screen [Presence] in Serum or Plasma

375

2.24

3.71

4.0

3.7

—

(40768797) Stomach Pathology biopsy report

113

2.49

3.35

1.1

1.2

—

(3016431) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Serum or Plasma

377

1.96

2.71

10.8

7.0

1.2

mmol/l

0.28

325

(3043405) Microscopic observation [Identifier] in Specimen by Non-gynecological cytology method

5.73

2.58

1.8

1.2

—

(3034770) Mitochondria Ab [Titer] in Serum

3.69

2.32

1.4

1.2

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

2.76

2.18

2.5

2.3

—

(43054903) Holo-transcobalamin II [Moles/volume] in Serum

294

1.82

2.17

2.3

1.9

89.4

96.1

pmol/l

0.44

134

(40768804) Tissue Pathology biopsy report

323

1.80

2.12

2.7

2.0

—

(3015399) Transferrin receptor.soluble [Mass/volume] in Serum or Plasma

168

1.93

2.11

3.0

1.9

3.1

3.2

mg/l

0.01

148

(3013650) Neutrophils [#/volume] in Blood by Automated count

472

1.77

1.97

8.6

10.0

4.9

4.2

e9/l

1.25

412

(3035350) Ketones [Presence] in Urine by Test strip

376

1.74

1.94

5.1

3.9

0.0

estimate

—

(3001604) Monocytes [#/volume] in Blood

386

1.74

1.93

6.3

5.8

0.6

e9/l

0.03

342

(3017143) Hepatitis C virus Ab [Presence] in Serum

2.10

1.91

1.6

—

(3006315) Basophils [#/volume] in Blood

387

1.73

1.91

6.4

5.9

0.1

0.0

e9/l

1.01

342

(3037467) Urinalysis macro (dipstick) panel - Urine

528

1.77

1.84

5.3

4.2

—

(3019198) Lymphocytes [#/volume] in Blood

392

1.70

1.78

6.3

5.8

1.8

e9/l

0.12

357

(3009261) Glucose [Presence] in Urine by Test strip

383

1.69

1.77

5.2

3.8

0.0

estimate

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

2.23

1.68

1.1

1.3

—

(46237023) Hepatitis B virus core and surface Ab and surface Ag panel - Serum

2.93

1.68

1.4

1.2

—

(46236098) ABO and Rh group [Type] in Blood by Confirmatory method

172

1.79

1.66

2.4

2.2

—

(3012110) Lysozyme [Mass/volume] in Serum or Plasma

3.70

1.63

1.8

1.4

8.8

13.0

mg/l

—

(3049717) Cytology report of Urine Cyto stain

2.82

1.61

2.0

2.8

—

(3013115) Eosinophils [#/volume] in Blood

400

1.64

1.59

6.7

6.0

0.2

e9/l

1.04

360

(3015736) pH of Urine

298

1.65

1.57

4.8

3.6

—

(3010521) Mycoplasma pneumoniae IgM Ab [Presence] in Serum by Immunoassay

2.97

1.53

1.3

1.1

—

(3041942) Cyclic citrullinated peptide Ab [Units/volume] in Serum

127

1.83

1.52

1.2

1.3

1.1

10.9

u/ml

1.74

(3019284) Hepatitis B virus surface Ag [Presence] in Serum

104

1.90

1.49

1.7

1.5

—

(3019250) Coagulation factor VIII activity actual/normal in Platelet poor plasma by Coagulation assay

3.23

1.45

2.4

2.6

237.0

183.0

—

(3043109) Cytology report of Tissue fine needle aspirate Cyto stain

3.23

1.45

1.0

1.2

—

(3021601) Nitrite [Presence] in Urine by Test strip

379

1.59

1.42

8.2

5.4

0.0

estimate

—

(36031861) Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection

2.26

1.38

1.1

1.8

—

(3048689) Calprotectin [Mass/mass] in Stool

1.88

1.35

2.4

1.9

136.1

157.5

ug/g

—

(3021589) Normoblasts [#/volume] in Blood

354

1.56

1.35

11.3

9.6

0.0

e9/l

0.00

291

(3000330) Specific gravity of Urine by Test strip

2.20

1.34

4.2

4.7

—

(40771025) 25-Hydroxyvitamin D3+25-Hydroxyvitamin D2 [Moles/volume] in Serum or Plasma

317

1.57

1.33

2.9

2.3

70.7

76.0

nmol/l

0.76

275

(3020460) C reactive protein [Mass/volume] in Serum or Plasma

795

2.05

1.33

18.5

14.0

26.2

23.2

mg/l

0.29

612

(3032080) INR in Blood by Coagulation assay

318

1.56

1.31

6.4

7.3

1.1

1.2

inr

—

100

(3048929) Epstein Barr virus Ab [Presence] in Serum

2.87

1.30

1.6

1.3

—

(3000850) Epithelial cells [#/volume] in Urine

168

1.66

1.26

5.6

2.4

11.4

5.8

e6/l

0.38

151

(3029287) Urinalysis microscopic panel [#/volume] - Urine by Automated count

293

1.55

1.25

6.0

3.0

—

(3027545) Mycoplasma pneumoniae Ab [Presence] in Serum by Immunoassay

2.72

1.23

1.6

1.3

—

(40760892) CBC W Ordered Manual Differential panel - Blood

178

1.63

1.22

6.1

5.1

—

(3003694) ABO and Rh group [Type] in Blood

213

1.59

1.22

1.5

1.3

—

(46236952) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (MDRD)

1.97

1.12

4.1

3.5

54.4

57.5

ml/min/173m2

—

(3024135) Streptococcus.beta-hemolytic [Presence] in Throat by Organism specific culture

115

1.69

1.09

1.4

1.3

—

(3044640) Blood type and Crossmatch panel - Blood

238

1.51

1.05

3.3

2.3

—

(40768793) Breast Pathology biopsy report

2.34

1.04

1.4

1.2

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

1.96

1.04

1.6

1.3

—

(3009542) Hematocrit [Volume Fraction] of Blood

732

1.61

0.98

20.7

14.6

38.7

39.9

0.50

523

(3007853) Bacteria identified in Skin by Aerobe culture

1.73

0.97

1.3

1.5

—

(3021614) Rheumatoid factor [Units/volume] in Serum or Plasma

136

1.59

0.96

1.2

1.3

13.0

37.7

iu/ml

—

(3030467) Casts [#/volume] in Urine by Automated count

233

1.48

0.96

6.7

3.0

0.4

0.5

e6/l

0.10

176

(3019550) Sodium [Moles/volume] in Serum or Plasma

813

1.81

0.96

22.2

15.9

139.6

139.7

mmol/l

0.16

786

(3041096) Erythrocytes [Presence] in Urine by Automated

225

1.48

0.94

5.5

3.5

—

(3013742) Prealbumin [Mass/volume] in Serum or Plasma

1.79

0.94

2.5

2.4

0.3

0.2

g/l

2.23

(3017895) Helicobacter pylori Ab [Units/volume] in Serum

2.22

0.93

1.5

1.6

—

(3021337) Troponin I.cardiac [Mass/volume] in Serum or Plasma

146

1.56

0.92

3.2

3.0

2894.8

109.8

ng/l

0.46

115

(3020564) Creatinine [Moles/volume] in Serum or Plasma

841

1.86

0.92

23.0

16.5

81.5

77.2

umol/l

0.48

841

(3014162) Mycobacterium tuberculosis DNA [Presence] in Specimen by NAA with probe detection

2.14

0.91

1.3

2.1

—

(3023103) Potassium [Moles/volume] in Serum or Plasma

816

1.77

0.90

21.1

15.9

4.0

mmol/l

0.08

788

(36304419) Bacteria [Presence] in Urine

228

1.46

0.88

6.7

2.9

—

(3023368) Bacteria identified in Blood by Culture

210

1.47

0.87

4.8

4.1

—

(3019050) Tissue transglutaminase IgA Ab [Units/volume] in Serum

176

1.48

0.83

1.2

0.4

1.0

u/ml

—

(3051552) Clostridioides difficile toxin genes [Presence] in Stool by NAA with probe detection

1.81

0.83

1.6

—

(3022145) Colonoscopy Study observation

1.63

0.80

1.6

1.2

—

(3004248) Sex hormone binding globulin [Moles/volume] in Serum or Plasma

0.00

0.80

0.0

1.5

—

36.2

—

(3020630) Protein [Mass/volume] in Serum or Plasma

1.72

0.79

1.4

3.2

68.4

67.2

g/l

0.29

(3004588) Protein electrophoresis panel - Serum or Plasma

1.77

0.78

1.1

3.1

—

(3049804) Myeloperoxidase IgG Ab [Units/volume] in Serum

2.23

0.77

1.4

1.1

—

(40763086) Leukocyte esterase [Presence] in Urine by Automated test strip

299

1.38

0.76

5.3

3.9

—

(3005719) IgG [Mass/volume] in Serum or Plasma

1.74

0.75

1.3

2.4

10.2

10.3

g/l

—

(3005013) Prostate Specific Ag Free [Mass/volume] in Serum or Plasma

162

1.46

0.75

2.3

2.8

0.6

0.7

ug/l

0.72

108

(3006418) Campylobacter sp identified in Tissue by Organism specific culture

1.97

0.71

1.0

1.3

—

(3014765) Yersinia sp identified in Stool by Organism specific culture

1.97

0.71

1.0

1.3

—

(42529406) Shigella sp [Presence] in Stool by Culture

1.97

0.71

1.0

1.3

—

(3002582) Erythrocytes [#/volume] in Urine

255

1.38

0.71

6.8

3.0

39.0

41.9

e6/l

0.03

198

(3030306) Epithelial cells.non-squamous [#/volume] in Urine by Automated count

146

1.46

0.71

4.3

2.8

4.1

1.2

e6/l

0.39

(3008898) HLA-B27 [Presence]

1.90

0.69

1.0

1.1

—

(3026782) Osmolality of Urine

157

1.43

0.66

4.5

3.0

594.0

557.6

mosm/kgh2o

0.22

135

(3018095) Leukocytes [#/volume] in Urine

286

1.35

0.66

7.9

3.7

63.8

68.8

e6/l

0.03

207

(3013603) Prostate specific Ag [Mass/volume] in Serum or Plasma

270

1.34

0.61

4.1

4.8

2.1

2.3

ug/l

0.09

236

(3021584) Pregnancy associated plasma protein A [Units/volume] in Serum or Plasma

0.00

0.61

0.0

1.4

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.61

0.0

1.8

—

(3042194) Human metapneumovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.61

0.0

1.8

—

(3025941) Bacteria identified in Stool by Culture

1.52

0.59

1.6

1.2

—

(3045783) Sodium and Potassium panel [Moles/volume] - Serum or Plasma

1.49

0.56

7.2

7.7

—

(3021879) Hepatitis B virus core Ab [Presence] in Serum

1.55

0.56

1.3

1.5

—

(3005322) IgE [Units/volume] in Serum or Plasma

1.62

0.55

1.2

200.1

134.2

u/ml

—

(3020682) Albumin/Creatinine [Ratio] in Urine

246

1.32

0.55

4.9

3.8

7.2

9.9

mg/mmol

0.20

146

(3001784) Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma

219

1.32

0.53

3.0

4.3

22.8

23.2

0.06

110

(42870588) Differential panel, method unspecified - Blood

248

1.30

0.51

6.9

5.4

—

(40762366) Oxygen capacity [Volume Fraction] in Arterial blood

1.60

0.50

7.1

6.0

—

(3009035) Cobalamin (Vitamin B12) [Moles/volume] in Serum or Plasma

158

1.33

0.46

1.8

471.5

475.8

pmol/l

0.02

134

(3012516) Albumin [Mass/volume] in Urine

235

1.27

0.43

4.0

3.1

2560.9

72.7

mg/l

0.48

142

(40765161) Human bocavirus DNA [Presence] in Specimen by NAA with probe detection

0.00

0.41

0.0

1.9

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.41

0.0

1.6

—

(3019225) pH of Specimen

1.34

0.40

3.0

5.0

—

(3000991) Gas panel - Venous blood

1.38

0.39

15.0

6.7

—

(3040853) Adenovirus DNA [Identifier] in Specimen by NAA with probe detection

0.00

0.39

0.0

1.8

—

(40758558) Short blood count panel - Blood

201

1.26

0.37

5.3

7.8

—

(3011397) Hemoglobin [Presence] in Urine by Test strip

173

1.27

0.37

4.3

3.6

—

(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

1.49

0.37

1.5

1.8

—

(3027273) Bicarbonate [Moles/volume] in Venous blood

1.46

0.36

2.5

3.9

25.5

24.6

mmol/l

—

(586526) SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with probe detection

1.46

0.36

1.5

1.3

—

(3004529) Oxygen [Partial pressure] adjusted to patient's actual temperature in Venous blood

1.39

0.35

3.3

4.2

35.8

48.5

—

(43534045) MCM6 gene c.-13910C>T and -13915T>G [Identifier] in Blood or Tissue by Molecular genetics method Nominal

1.32

0.33

1.0

—

(3029879) Epithelial cells.squamous [#/volume] in Urine by Automated count

138

1.28

0.33

4.7

2.9

0.2

3.0

e6/l

—

(1761868) Lipid panel - Serum or Plasma

290

1.21

0.33

3.8

3.1

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

1.40

0.32

33.0

7.4

0.7

0.6

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

1.37

0.32

33.0

7.3

1.2

1.7

—

(3013512) EKG study

227

1.20

0.27

4.3

4.0

—

(4035726)

1.33

0.27

1.8

1.2

—

(3043924) Respiratory syncytial virus RNA [Identifier] in Specimen by NAA with probe detection

1.28

0.26

1.5

1.6

—

(3038288) Influenza virus B RNA [Presence] in Specimen by NAA with probe detection

1.28

0.26

1.5

1.7

—

(3012544) pH of Venous blood

1.20

0.25

9.3

3.7

—

(3021960) Folate [Moles/volume] in Serum or Plasma

182

1.20

0.24

1.9

1.5

17.3

22.7

nmol/l

1.42

149

(40761511) CBC panel - Blood by Automated count

835

1.24

0.23

19.2

12.9

—

(3020565) Legionella pneumophila DNA [Presence] in Specimen by NAA with probe detection

0.00

0.21

0.0

1.6

—

(3028531) Enolase.neuron specific [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.8

—

13.6

—

(3019145) Choriogonadotropin.beta subunit free [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.5

—

(3030692) Respiratory virus DNA+RNA [Identifier] in Specimen by NAA with probe detection

0.00

0.21

0.0

1.5

—

(36033641) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay

0.00

0.21

0.0

2.1

—

(3042596) Human coronavirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.21

0.0

1.5

—

(3049506) Microalbumin [Mass/time] in Urine collected for unspecified duration

0.00

0.21

0.0

2.2

—

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

0.21

0.0

1.2

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.21

0.0

1.4

—

(3051651) Icteric interference index of Serum or Plasma

0.00

0.21

0.0

3.1

—

(3003181) Sodium [Moles/volume] in Urine

0.00

0.21

0.0

1.5

—

60.0

—

(3051611) Lipemic interference index of Serum or Plasma

0.00

0.21

0.0

3.1

—

(3004616) Nuclear Ab [Presence] in Serum

0.00

0.21

0.0

1.2

—

(3050129) First trimester maternal screen panel - Serum or Plasma

0.00

0.21

0.0

1.2

—

(3014702) Chromogranin A [Moles/volume] in Serum or Plasma

0.00

0.21

0.0

2.5

—

3.4

—

(3012477) Bordetella pertussis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.20

0.0

1.6

—

(3031478) Chlamydophila pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.20

0.0

1.7

—

(3016701) Glucose [Moles/volume] in Serum or Plasma --2 hours post dose glucose

0.00

0.20

0.0

1.2

—

7.7

—

(3044889) 12 lead EKG panel

572

1.13

0.18

4.4

3.8

—

(40761535) Cells panel - Urine sediment

1.14

0.17

2.0

3.0

—

(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma

0.73

0.17

1.2

1.8

—

(3000492) Spirometry study

1.14

0.16

1.4

1.5

—

(3019902) Methicillin resistant Staphylococcus aureus [Presence] in Specimen by Organism specific culture

1.17

0.16

3.1

3.6

—

(3015377) Calcium [Moles/volume] in Serum or Plasma

267

1.12

0.15

3.3

3.6

2.3

2.4

mmol/l

0.32

237

(43054914) Glucose tolerance 2 hours panel - Serum or Plasma

0.78

0.15

1.0

1.6

—

(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma

317

1.11

0.14

3.7

4.0

35.9

34.3

ng/l

0.03

221

(3000963) Hemoglobin [Mass/volume] in Blood

883

1.24

0.14

30.5

20.7

132.0

135.7

g/l

1.24

863

(3035941) MCH [Entitic mass]

883

1.24

0.14

30.2

20.4

30.1

30.3

0.59

863

(3024731) MCV [Entitic volume]

882

1.25

0.14

30.2

20.5

90.4

91.1

0.80

862

(3026008) Bacteria identified in Urine by Culture

240

1.11

0.13

2.4

3.0

—

(706163) SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection

492

0.91

0.12

2.8

3.0

—

(3044938) Influenza virus A RNA [Presence] in Specimen by NAA with probe detection

124

1.15

0.12

1.4

1.8

—

(3004716) Salmonella sp identified in Stool by Organism specific culture

1.17

0.10

1.0

1.3

—

(3044491) Cholesterol non HDL [Mass/volume] in Serum or Plasma

1.12

0.10

1.2

1.6

—

(4010399)

1.14

0.09

1.3

1.4

—

(36660697) Celiac disease serology panel - Serum

1.12

0.09

1.0

1.1

—

(3005785) Creatine kinase.MB [Mass/volume] in Serum or Plasma

0.84

0.08

1.8

2.0

1.6

5.0

ug/l

—

(3018006) Microscopic observation [Identifier] in Cervix by Cyto stain.thin prep

119

1.11

0.06

1.5

1.3

—

(3029937) Albumin [Presence] in Urine by Test strip

202

1.05

0.02

5.2

3.9

0.0

estimate

—

(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)

754

1.04

0.00

19.6

13.5

81.3

81.1

ml/min/173m2

0.02

605

(3042936) Bacteria identified in Isolate by Culture

118

1.02

0.00

2.8

1.8

—

(3000494) Fungus identified in Specimen by Culture

1.01

0.00

1.0

1.4

—

(46235355) HIV 1 and 2 tests - Meaningful Use set

126

1.04

0.00

1.9

1.8

—

(3045142) Bone marrow Pathology biopsy report

0.00

0.0

1.3

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.0

1.2

—

(3029075) Extractable nuclear Ab panel - Serum

0.00

0.0

1.0

—

(40763531) Fetal Nuchal fold [Multiple of the median] Thickness adjusted for maternal weight

0.00

0.0

1.2

—

(3022803) Oxygen [Partial pressure] adjusted to patient's actual temperature in Arterial blood

0.00

0.0

4.0

—

(40764126) Parainfluenza virus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.5

—

(3013201) Beta-2-Microglobulin [Mass/volume] in Serum or Plasma

0.00

0.0

1.9

—

3.4

—

(3023511) Choriogonadotropin [Units/volume] in Urine

0.00

0.0

1.6

—

(3045156) Carbon dioxide [Partial pressure] adjusted to patient's actual temperature in Arterial blood

0.00

0.0

4.0

—

(44790047)

0.00

0.0

1.6

—

(3008714) Choriogonadotropin [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.2

—

(44790049)

0.00

0.0

1.6

—

(44790048)

0.00

0.0

1.6

—

(46235831) Pregnancy associated plasma protein A [Multiple of the median] adjusted in Serum or Plasma

0.00

0.0

1.2

—

(3049207) Fetal Trisomy 21 risk [Likelihood] Based on maternal age

0.00

0.0

1.2

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.0

1.2

—

(3041423) Sjogrens syndrome-A extractable nuclear 60kD Ab [Units/volume] in Serum

0.00

0.0

1.1

—

(4146454)

0.00

0.0

2.3

—

(44806118)

0.00

0.0

1.6

—

(4281824)

0.00

0.0

1.0

—

(3017704) Immunofixation for Urine

0.00

0.0

1.7

—

(43055361) Metamyelocytes/Leukocytes [Pure number fraction] in Blood by Manual count

0.00

0.0

3.9

—

(3021125) Hepatitis C virus RNA [Presence] in Serum or Plasma by NAA with probe detection

0.00

0.0

1.6

—

(3026515) Parvovirus B19 IgM Ab [Units/volume] in Serum

0.00

0.0

1.4

—

(40766048) U1 small nuclear ribonucleoprotein 70kD Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.3

—

(1002102) Choriogonadotropin.intact+Beta subunit [Mass/volume] in Serum or Plasma

0.00

0.0

1.3

—

(44816844) Macroprolactin [Units/volume] in Serum or Plasma

0.00

0.0

1.2

—

(3041642) Human coronavirus 229E RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.4

—

(3000081) cloZAPine [Moles/volume] in Serum or Plasma

0.00

0.0

14.6

—

1329.6

—

(1001509) Gas and Carbon monoxide and Electrolytes panel - Arterial blood

0.00

0.0

2.2

—

(3047189) Immunofixation for 24 hour Urine

0.00

0.0

1.6

—

(3035933) Granulocytes/100 leukocytes in Blood

0.00

0.0

1.0

—

(40764127) Haemophilus influenzae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.6

—

(40761536) Microorganisms panel - Urine sediment

0.89

0.00

10.3

3.4

—

(3037875) Bordetella parapertussis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.6

—

(3011391) Calcitriol [Moles/volume] in Serum or Plasma

0.00

0.0

1.8

—

(3038546) Human coronavirus OC43 RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.4

—

(40758897) Direct antiglobulin test.IgG specific reagent [Presence] on Red Blood Cells

0.00

0.0

2.7

—

(3014791) Apolipoprotein B [Mass/volume] in Serum or Plasma

0.00

0.0

1.8

—

1.0

—

(3016018) Differential panel - Cerebral spinal fluid

0.00

0.0

1.0

—

(3040359) Human coronavirus NL63 RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.4

—

(40762485) Glomerular basement membrane Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.1

—

(3032699) Streptococcus pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.5

—

(3027953) Aldolase [Enzymatic activity/volume] in Serum or Plasma

0.00

0.0

1.2

—

11.4

—

(3024950) Chlamydia trachomatis DNA [Presence] in Urine by NAA with probe detection

0.87

0.00

1.3

1.8

—

(3000034) Microalbumin [Mass/volume] in Urine

0.00

0.0

3.3

—

31.8

—

(3008832) Norclozapine [Moles/volume] in Serum or Plasma

0.00

0.0

10.6

—

897.8

—

(3021236) Streptolysin O Ab [Units/volume] in Serum or Plasma

0.00

0.0

1.5

—

73.2

—

(40758895) Direct antiglobulin test.complement C3d specific reagent [Presence] on Red Blood Cells

0.00

0.0

2.7

—

(3002619) Bacteria identified in Specimen by Culture

0.00

0.0

1.0

—

(3025023) Rhinovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.3

—

(3037556) Urate [Mass/volume] in Serum or Plasma

0.00

0.0

1.0

—

(3019832) Treponema pallidum Ab [Presence] in Serum

1.00

0.00

1.8

1.7

—

(36306090) Helicobacter pylori [Presence] in Tissue by Organism specific culture

0.00

0.0

1.0

—

(3011166) Borrelia burgdorferi Ab [Presence] in Cerebral spinal fluid

0.00

0.0

1.0

—

(3024263) Appearance of Synovial fluid

0.00

0.0

1.0

—

(3035999) Lactate [Moles/volume] in Cerebral spinal fluid

0.00

0.0

1.2

—

1.8

—

(3036432) Mycobacterium tuberculosis genotype [Identifier] in Isolate

0.00

0.0

10.0

—

(3045066) Thymidine kinase [Enzymatic activity/volume] in Serum

0.00

0.0

1.2

—

37.4

—

(3003510) Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection

0.87

0.00

1.2

1.8

—

(3014326) Insulin-like growth factor-I [Moles/volume] in Serum or Plasma

0.00

0.0

2.1

—

19.2

—

(3016436) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma

0.00

0.0

6.6

—

231.2

—

(4027681)

0.00

0.0

1.2

—

(3009550) Parvovirus B19 IgG Ab [Titer] in Serum

0.00

0.0

1.4

—

Mortality – FinRegistry

↥

Association

Association between endpoint CD2_BENIGN_EXTRAHEPATIC_BILE and mortality.

Females

Parameter	HR [95% CI]	p-value
CD2_BENIGN_EXTRAHEPATIC_BILE	1.636 [1.22, 2.19]	< 0.001
Birth year	0.997 [0.99, 1.01]	0.484

During the follow-up period (1.1.1998 — 31.12.2019), 62 out of 312 females with CD2_BENIGN_EXTRAHEPATIC_BILE died.

Males

Parameter	HR [95% CI]	p-value
CD2_BENIGN_EXTRAHEPATIC_BILE	1.638 [1.19, 2.25]	0.002
Birth year	0.989 [0.98, 1.0]	0.018

During the follow-up period (1.1.1998 — 31.12.2019), 67 out of 232 males with CD2_BENIGN_EXTRAHEPATIC_BILE died.

Mortality risk

Mortality risk for people of age

years, who have CD2_BENIGN_EXTRAHEPATIC_BILE.

N-year risk	Females	Males
1	0.216%	0.35%
5	1.007%	2.019%
10	2.387%	5.015%
15	4.663%	9.497%
20	8.047%	15.926%

Relationships between endpoints

↥

Index endpoint: CD2_BENIGN_EXTRAHEPATIC_BILE – Benign neoplasm: Extrahepatic bile ducts

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

rg [CI]

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

Benign neoplasm: Extrahepatic bile ducts

Endpoint definition

Endpoint definition steps

FinnGen

Phenotype data

1. Apply sex-specific rule

2. Check conditions

3. Check pre-conditions, main-only, mode, registry filters

4. Check minimum number of events

5. Include endpoints

6. Filter based on genotype QC (FinnGen only)

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

Key figures

-FinnGen-

Key figures

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

Matched cohort

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints