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.

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Endpoint definition

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Report an error or suggest an improvement for this endpoint codes

Endpoint definition steps	FinnGen
Phenotype data	557745
1. Apply sex-specific rule None	557745
2. Check conditions None	557745
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.	129
4. Check minimum number of events None	129
5. Include endpoints None	129
6. Filter based on genotype QC (FinnGen only)	117

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:

None

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	117	66	51
Unadjusted period prevalence (%)	0.02	0.02	0.02
Median age at first event (years)	61.70	58.70	65.58

-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

↥

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
120: Matched controls
1200

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

D13.5

ICD-10 Finland

Benign neoplasm: Extrahepatic bile ducts

+∞

159.9

115

JKA21

NOMESCO Finland

Laparoscopic cholecystectomy

11.3

39.5

K82.8

ICD-10 Finland

Other specified diseases of gallbladder

+∞

13.8

D37.6

ICD-10 Finland

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

19.0

12.1

JN1AE

NOMESCO Finland

Ultrasound examination of upper part of abdomen

5.2

10.6

JJ1CE

NOMESCO Finland

Liver, bile duct and pancreas endoscopic ultrasound examination

108.2

9.6

UJK02

NOMESCO Finland

ERCP

12.1

9.1

JKE98

NOMESCO Finland

Other transduodenal endoscopic operation on bile duct or ampulla of Vater

14.6

7.6

JL5BG

NOMESCO Finland

MRI examinaiton of bile and pancreas ducts with high intesity magnet

12.0

7.5

R10.4

ICD-10 Finland

Other and unspecified abdominal pain

2.9

7.4

295

D37.7

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Other digestive organs

8.6

6.8

JN1CG

NOMESCO Finland

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

11.0

6.7

K80.2

ICD-10 Finland

Calculus of gallbladder without cholecystitis

3.4

6.7

JL5SB

NOMESCO Finland

Endoscopic retrograd cholangiopancreaticography

15.4

6.5

K82.4

ICD-10 Finland

Cholesterolosis of gallbladder

73.6

6.5

K83.8

ICD-10 Finland

Other specified diseases of biliary tract

+∞

6.3

UJK12

NOMESCO Finland

Peroral cholangioscopy

+∞

6.3

WX402

NOMESCO Finland

General anaesthesia

2.8

6.1

168

LabWAS

↥

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

138

3.57

8.85

2.4

4.8

2.77

10.73

ug/l

1.53

108

(3002256) Pathology report gross observation

130

3.25

7.17

1.3

—

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

497

2.36

4.86

3.1

2.6

—

estimate

—

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

569

2.06

3.46

4.9

3.9

0.00

estimate

-0.00

109

(3021589) Normoblasts [#/volume] in Blood

475

2.00

3.38

13.2

12.2

0.00

e9/l

-0.00

391

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

574

2.03

3.32

4.9

3.9

0.00

estimate

-0.00

101

(40768797) Stomach Pathology biopsy report

151

2.21

3.15

1.1

1.3

—

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

563

1.89

2.80

5.0

3.9

0.00

estimate

-0.00

109

(3019601) Blood group antibody investigation [Interpretation] in Plasma or RBC

6.25

2.73

1.3

1.2

—

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

531

1.83

2.61

11.4

7.9

1.21

mmol/l

0.03

458

(3026285) Alpha 1 antitrypsin [Mass/volume] in Serum or Plasma

5.20

2.43

1.0

1.47

1.46

g/l

—

(3032773) Endomysium IgG Ab [Titer] in Serum

6.46

2.39

1.0

—

(40768804) Tissue Pathology biopsy report

426

1.76

2.38

2.7

2.0

—

(3041096) Erythrocytes [Presence] in Urine by Automated

328

1.77

2.33

4.7

3.3

0.00

estimate

-0.00

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

4.80

2.30

1.8

1.4

—

(3015916) Alpha-1-Fetoprotein [Units/volume] in Serum or Plasma

4.06

2.29

1.3

1.6

2.14

6.18

u/ml

—

(40763571) Iron/Transferrin [Ratio] in Serum or Plasma

162

1.95

2.28

3.4

2.5

24.77

23.79

0.16

155

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

178

1.91

2.27

1.4

21.91

8.22

u/ml

0.33

(3001604) Monocytes [#/volume] in Blood

555

1.74

2.26

6.8

6.2

0.58

0.59

e9/l

0.24

485

(3006315) Basophils [#/volume] in Blood

558

1.73

2.19

6.7

6.2

0.05

0.04

e9/l

0.67

484

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

622

1.73

2.11

9.2

10.8

4.57

4.14

e9/l

0.86

540

(3019198) Lymphocytes [#/volume] in Blood

562

1.70

2.10

6.8

6.2

1.87

1.83

e9/l

0.14

506

(3013115) Eosinophils [#/volume] in Blood

574

1.69

2.06

6.8

6.5

0.23

0.18

e9/l

1.16

508

(3007853) Bacteria identified in Skin by Aerobe culture

122

1.98

2.01

1.5

1.8

—

(40760892) CBC W Ordered Manual Differential panel - Blood

252

1.74

2.00

5.6

4.9

—

(3034770) Mitochondria Ab [Titer] in Serum

2.70

1.99

1.3

1.1

—

(3015736) pH of Urine

452

1.65

1.96

4.2

3.6

6.33

6.14

0.59

262

(3038177) Helicobacter pylori Ab [Presence] in Serum

3.89

1.96

1.0

1.3

—

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

203

1.79

1.95

1.3

25.00

30.91

iu/ml

0.19

(3045414) Leukocytes [Presence] in Urine

2.08

1.92

1.4

1.9

0.00

estimate

—

(3032080) INR in Blood by Coagulation assay

506

1.62

1.82

10.2

10.3

1.11

1.19

inr

0.77

408

(3049717) Cytology report of Urine Cyto stain

2.62

1.78

1.8

2.8

—

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

304

1.65

1.76

5.9

3.2

0.33

0.45

e6/l

0.20

222

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

136

1.86

1.75

1.8

1.5

—

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

2.31

1.74

2.7

2.6

—

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

436

1.59

1.68

4.8

3.8

0.00

estimate

-0.00

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

3.27

1.68

1.0

1.2

—

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

2.39

1.60

1.6

11.66

11.81

u/ml

—

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

252

1.61

1.51

2.8

2.0

3.14

2.93

mg/l

0.11

219

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

110

1009

2.08

1.42

21.4

16.5

22.66

24.25

mg/l

0.18

818

(1761482) Bacteria [#/volume] in Urine by Culture

2.50

1.41

3.3

6.0

—

(3014576) Chloride [Moles/volume] in Serum or Plasma

162

1.69

1.40

15.7

7.9

105.44

104.41

mmol/l

0.45

162

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

2.29

1.40

1.3

2.5

—

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

257

1.57

1.39

3.3

2.3

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

2.07

1.38

1.6

1.5

—

(3014051) Protein [Presence] in Urine by Test strip

322

1.52

1.34

4.5

3.2

—

0.25

—

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

156

1.67

1.33

1.5

—

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

156

1.67

1.33

1.9

1.5

—

(3005702) Mycobacterium sp identified in Specimen by Organism specific culture

2.58

1.32

1.5

—

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

100

1.82

1.32

3.4

3.0

68.56

67.44

g/l

0.30

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

111

1033

1.99

1.31

24.7

19.2

139.68

139.71

mmol/l

0.03

111

1015

(3007844) Epstein Barr virus capsid IgM Ab [Units/volume] in Serum by Immunoassay

2.85

1.30

1.6

1.3

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

1.83

1.29

1.2

1.4

—

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

2.47

1.26

1.8

1.4

—

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

254

1.53

1.25

1.2

1.3

0.59

1.69

u/ml

1.02

(3021952) Alkaline phosphatase isoenzymes [Enzymatic activity/volume] in Serum or Plasma by Heat stability

2.70

1.23

1.4

—

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

2.37

1.20

1.5

1.2

—

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

111

1034

1.98

1.19

23.9

19.3

3.96

3.98

mmol/l

0.16

111

1012

(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

1.99

1.16

2.5

1.8

—

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

2.05

1.15

2.2

4.2

25.32

24.45

mmol/l

—

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

295

1.48

1.14

1.6

1.4

—

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

1.75

1.13

2.3

2.6

0.24

0.21

g/l

0.78

(3010130) Cytomegalovirus IgG Ab [Units/volume] in Serum or Plasma

2.44

1.10

1.6

1.2

—

187.43

—

(3002582) Erythrocytes [#/volume] in Urine

353

1.44

1.08

6.4

3.3

29.91

40.52

e6/l

0.20

273

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

299

1.45

1.05

4.7

3.9

0.00

estimate

-0.00

(3048689) Calprotectin [Mass/mass] in Stool

132

1.62

1.05

2.6

2.2

116.04

143.47

ug/g

0.13

106

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

469

1.41

1.05

3.2

2.5

71.82

76.17

nmol/l

0.75

416

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

2.12

1.04

1.4

1.2

—

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

433

1.40

1.01

3.6

4.0

28.11

34.55

ng/l

0.21

307

(3001122) Ferritin [Mass/volume] in Serum or Plasma

472

1.40

1.00

4.0

2.7

142.91

121.03

ug/l

0.51

434

(3018095) Leukocytes [#/volume] in Urine

396

1.40

0.99

7.7

4.1

51.05

62.41

e6/l

0.11

279

(3044640) Blood type and Crossmatch panel - Blood

340

1.41

0.98

3.8

2.3

—

(3007164) IgA [Mass/volume] in Serum or Plasma

231

1.46

0.96

1.5

2.28

2.68

g/l

0.75

139

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

240

1.45

0.96

5.2

2.6

9.46

5.40

e6/l

0.37

219

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

179

1.50

0.94

4.5

3.3

0.43

2.68

e6/l

1.96

(3000991) Gas panel - Venous blood

103

1.64

0.93

11.4

9.1

—

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

1.79

0.89

3.5

3.9

36.37

49.27

0.92

(3008037) Lactate [Moles/volume] in Venous blood

2.05

0.88

2.0

3.3

1.38

1.35

mmol/l

—

(3013512) EKG study

377

1.36

0.83

3.8

3.5

—

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

1.66

0.82

1.5

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.80

0.0

1.5

—

(3015635) Cytomegalovirus IgM Ab [Units/volume] in Serum or Plasma

2.22

0.77

2.0

1.3

—

(3004383) Neutrophil cytoplasmic Ab.classic [Titer] in Serum by Immunofluorescence

2.22

0.77

1.2

1.0

—

(3022145) Colonoscopy Study observation

126

1.50

0.76

1.6

1.3

—

(3017918) Cytomegalovirus IgG Ab [Titer] in Serum or Plasma

2.13

0.75

2.0

1.3

—

(3019977) pH of Arterial blood

136

1.47

0.72

14.7

8.6

7.44

7.42

—

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

198

1.40

0.72

4.3

3.2

3.59

1.08

e6/l

0.38

110

(3038515) Glucose [Moles/volume] in Venous blood

1.96

0.71

2.2

3.3

6.16

7.62

mmol/l

—

(3024891) Influenza virus A+B Ag [Presence] in Specimen

1.82

0.67

1.2

1.1

—

(3001334) Neutrophil cytoplasmic Ab [Units/volume] in Serum

1.63

0.66

1.4

1.0

—

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

456

1.29

0.66

2.4

2.1

90.77

96.64

pmol/l

0.47

218

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

1.58

0.65

22.3

10.3

0.57

0.65

0.42

(3004588) Protein electrophoresis panel - Serum or Plasma

1.56

0.62

4.0

3.0

—

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

1.56

0.62

4.0

3.1

54.40

61.10

ml/min/173m2

—

(40768793) Breast Pathology biopsy report

1.69

0.62

1.4

1.3

—

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

1.69

0.62

1.0

1.3

—

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

1.69

0.62

1.0

1.3

—

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

1.69

0.62

1.0

1.3

—

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

1.58

0.61

1.4

1.3

—

(3023368) Bacteria identified in Blood by Culture

288

1.30

0.60

5.4

4.4

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

1.53

0.59

22.3

10.1

1.02

1.54

1.16

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

112

1079

1.57

0.58

28.3

21.1

79.63

77.44

umol/l

0.26

112

1065

(3025941) Bacteria identified in Stool by Culture

1.59

0.57

1.6

1.2

—

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

1.65

0.56

1.5

1.1

—

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

1.50

0.54

1.7

1.6

—

(3018418) pH of Serum or Plasma

349

1.27

0.54

7.0

4.3

7.39

7.40

0.25

242

(40768443) Skin Pathology biopsy report

1.52

0.48

1.4

1.3

—

(3026008) Bacteria identified in Urine by Culture

316

1.25

0.47

2.7

3.1

—

(3020682) Albumin/Creatinine [Ratio] in Urine

364

1.24

0.47

4.6

3.9

7.82

12.10

mg/mmol

0.32

216

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

260

1.26

0.46

4.1

3.8

—

0.00

—

(4024509) Urine culture

1.40

0.45

2.3

1.9

—

(21494755) Public health laboratory ask at order entry panel

0.63

0.44

1.2

1.4

—

(3010156) C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method

1.64

0.43

1.2

1.6

8.02

2.14

mg/l

—

(3029511) Human papilloma virus DNA [Presence] in Specimen by NAA with probe detection

1.59

0.43

1.6

1.3

—

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

1.59

0.43

2.4

2.0

237.00

184.91

—

(40761511) CBC panel - Blood by Automated count

108

1041

1.37

0.41

20.7

14.4

—

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

1.38

0.41

4.7

2.4

11.89

10.43

g/l

0.32

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

0.41

0.0

1.3

—

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

0.00

0.41

0.0

1.5

—

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

0.00

0.41

0.0

3.6

—

2.95

—

(3004616) Nuclear Ab [Presence] in Serum

0.00

0.41

0.0

1.2

—

(1761868) Lipid panel - Serum or Plasma

399

1.20

0.40

4.0

3.3

—

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

227

1.24

0.39

3.4

3.5

20.56

195.87

ng/l

1.99

180

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

103

990

1.29

0.37

21.3

16.2

81.45

79.76

ml/min/173m2

0.38

911

(3016888) Borrelia burgdorferi IgG Ab [Units/volume] in Serum

0.63

0.37

1.8

1.3

—

38.17

—

(4035726) Immunohistochemistry procedure

109

1.32

0.35

1.6

1.3

—

(3000494) Fungus identified in Specimen by Culture

137

1.28

0.34

1.4

1.5

—

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

0.67

0.34

1.3

2.0

—

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

356

1.19

0.33

5.0

5.2

2.20

2.06

ug/l

0.12

314

(3020891) Body temperature

1.37

0.32

30.6

4.3

36.93

36.88

°c

—

(3051714) Fibrin D-dimer FEU [Mass/volume] in Platelet poor plasma

235

1.19

0.28

1.8

1.7

1.33

1.29

mg/l

0.02

189

(3012095) Magnesium [Moles/volume] in Serum or Plasma

192

0.81

0.28

7.1

3.0

0.86

0.81

mmol/l

0.48

182

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

0.65

0.26

1.2

2.0

—

(40761536) Microorganisms panel - Urine sediment

0.73

0.25

10.8

3.4

—

(3003327) Ova and parasites identified in Stool by Light microscopy

1.37

0.24

3.0

1.5

—

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

220

1.17

0.23

3.2

2.8

0.63

0.77

ug/l

0.91

138

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

201

1.18

0.23

1.7

1.8

452.33

466.19

pmol/l

0.10

173

(3022313) Gas panel - Capillary blood

1.29

0.23

3.8

3.2

—

(3008898) HLA-B27 [Presence]

1.29

0.23

1.0

1.1

—

(36304997) Mycobacterium tuberculosis stimulated gamma interferon release by CD4+ and CD8+ T-cells [Units/volume] in Blood

1.23

0.22

1.8

1.4

—

0.11

—

(3024731) MCV [Entitic mean volume] in Red Blood Cells

112

1099

1.29

0.22

34.6

24.8

90.78

91.34

0.65

112

1086

(3009542) Hematocrit [Volume Fraction] of Blood by calculation

112

1100

1.27

0.22

35.3

25.4

39.41

40.27

0.82

112

1087

(3000963) Hemoglobin [Mass/volume] in Blood

112

1100

1.27

0.22

35.1

25.0

132.22

135.04

g/l

1.07

112

1087

(3035941) MCH [Entitic mass]

112

1100

1.27

0.22

34.5

24.7

30.16

30.39

0.71

112

1087

(3014037) CD3+CD4+ (T4 helper) cells/cells in Blood

0.00

0.21

0.0

3.9

—

47.67

—

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

0.00

0.21

0.0

2.2

—

(37208534) Antinuclear antibody arbitrary concentration in serum

0.00

0.21

0.0

1.0

—

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

174

1.18

0.21

1.9

1.8

—

(3051651) Icteric interference index of Serum or Plasma

0.00

0.21

0.0

3.3

—

0.92

—

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

0.00

0.21

0.0

2.0

—

(3045142) Bone marrow Pathology biopsy report

0.00

0.21

0.0

1.2

—

(3026725) Estradiol (E2) [Moles/volume] in Serum or Plasma

0.00

0.21

0.0

1.5

—

0.17

—

(4281824) Cell count and differential, peritoneal fluid

0.00

0.21

0.0

1.0

—

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

1.26

0.20

1.7

1.3

—

(3001019) Free T4 and TSH panel - Serum or Plasma

1.24

0.20

1.3

1.4

—

(3032700) Glomerular basement membrane Ab [Units/volume] in Serum

0.00

0.20

0.0

1.1

—

(3046870) Tissue transglutaminase IgG Ab [Units/volume] in Serum

1.20

0.18

1.1

1.2

—

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

1.14

0.17

1.0

—

(3007628) Bicarbonate [Moles/volume] standard in Venous blood

1.17

0.17

11.5

3.1

23.90

24.76

mmol/l

—

(3019832) Treponema pallidum Ab [Presence] in Serum

1.12

0.16

1.9

—

(3042936) Bacteria identified in Isolate by Culture

169

1.15

0.16

2.3

1.9

—

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

607

0.91

0.15

3.2

3.0

—

(3012516) Albumin [Mass/volume] in Urine

358

1.09

0.12

4.1

3.3

51.02

70.05

mg/l

0.25

228

(42870588) Differential panel, method unspecified - Blood

359

1.09

0.11

7.2

6.0

—

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

134

1.14

0.11

2.1

1.8

—

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

106

1.15

0.10

3.1

3.5

—

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

127

1.12

0.08

8.5

6.8

—

(3024889) Methemoglobin/Hemoglobin.total in Venous blood

1.06

0.08

2.6

2.7

0.53

0.63

—

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

1.03

0.08

1.7

1.2

152.11

379.44

u/ml

—

(40761535) Cells panel - Urine sediment

1.03

0.07

2.1

3.1

—

(3025839) Triglyceride [Moles/volume] in Serum or Plasma

446

0.94

0.07

1.9

2.0

1.40

1.36

mmol/l

0.15

373

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

167

1.09

0.07

3.3

2.0

—

(3016293) Bicarbonate [Moles/volume] in Serum or Plasma

1.08

0.07

6.7

8.0

24.00

25.14

mmol/l

—

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

128

1.11

0.07

2.1

1.9

—

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

286

1.07

0.06

3.8

4.3

21.43

23.47

0.45

135

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

156

1.03

0.00

1.5

—

(3000492) Spirometry study

101

0.99

0.00

1.3

1.6

—

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

107

1.03

0.00

1.1

1.5

—

(3019150) Specific gravity of Urine by Refractometry

251

0.99

0.00

4.2

3.8

1.02

kg/l

0.97

163

(4146454) Self-monitoring of blood glucose

0.00

0.0

3.2

—

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

0.00

0.0

1.7

—

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

0.00

0.0

1.0

—

(40760543) Extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.2

—

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

0.00

0.0

4.9

—

9.82

—

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

0.00

0.0

4.9

—

4.56

—

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

0.00

-0.00

0.0

1.5

—

(3030429) Borrelia sp DNA [Identifier] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.0

—

(3002079) Sodium [Moles/time] in 24 hour Urine

0.00

-0.00

0.0

1.0

—

144.78

—

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

0.00

-0.00

0.0

1.5

—

84.12

—

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

0.00

-0.00

0.0

1.3

—

30.15

—

(4010399) Spirometry for bronchospasm with prolonged evaluation after bronchodilator

0.90

-0.00

1.5

1.4

—

(40759883) Oligoclonal Bands IgG [Presence] in Cerebral spinal fluid by Isoelectric focusing

0.00

-0.00

0.0

1.0

—

(3036432) Mycobacterium tuberculosis genotype [Identifier] in Isolate

0.00

-0.00

0.0

9.8

—

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

0.00

-0.00

0.0

1.5

—

73.17

—

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

0.00

-0.00

0.0

1.4

—

(3004451) EKG impression Narrative

0.00

-0.00

0.0

1.6

—

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

0.00

-0.00

0.0

1.1

—

10.31

—

(42529582) MDA5 Ab [Presence] in Serum by Line blot

0.00

-0.00

0.0

1.0

—

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

0.93

-0.00

1.7

2.1

1.87

5.62

ug/l

—

(3030136) 5-Hydroxyindoleacetate [Moles/volume] in Serum or Plasma

0.00

-0.00

0.0

4.1

—

69.71

—

(36660697) Celiac disease serology panel - Serum

0.95

-0.00

1.3

1.2

—

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

0.00

-0.00

0.0

2.4

—

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

0.00

-0.00

0.0

15.6

—

886.43

—

(3024263) Appearance of Synovial fluid

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

21.4

—

1564.57

—

(3034988) Calcium [Moles/volume] in Capillary blood

0.00

-0.00

0.0

1.2

—

1.20

—

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

0.00

-0.00

0.0

1.7

—

(3036071) Salmonella sp Ab [Titer] in Serum

0.00

-0.00

0.0

1.0

—

(42528593) TIF1-gamma Ab [Presence] in Serum by Line blot

0.00

-0.00

0.0

1.0

—

(3046896) Herpes virus 6 DNA [Presence] in Cerebral spinal fluid by NAA with probe detection

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.7

—

47.72

—

(42529598) SUMO-activating enzyme subunit 1 Ab [Presence] in Serum by Line blot

0.00

-0.00

0.0

1.0

—

(3013637) Mi-2 Ab [Presence] in Serum

0.00

-0.00

0.0

1.0

—

(3049714) Procollagen type I.N-terminal propeptide [Mass/volume] in Serum

0.00

-0.00

0.0

2.0

—

85.74

—

(42869547) Procollagen type III.N-terminal propeptide [Mass/volume] in Serum

0.00

-0.00

0.0

1.0

—

7.78

—

(3018301) Testosterone Free [Moles/volume] in Serum or Plasma

0.00

-0.00

0.0

1.0

—

183.56

—

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

0.00

-0.00

0.0

5.8

—

223.67

—

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

0.00

-0.00

0.0

1.1

—

(3020911) Cortisol [Moles/time] in 24 hour Urine

0.00

-0.00

0.0

1.5

—

60.50

—

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

0.00

-0.00

0.0

1.5

—

(3005757) Coagulation factor V activity actual/normal in Platelet poor plasma by Coagulation assay

0.00

-0.00

0.0

1.0

—

94.60

—

(21493690) Lymphocyte T-cell and B-cell and Natural killer subsets panel - Blood

0.00

-0.00

0.0

3.0

—

(40771527) Human papilloma virus E6+E7 mRNA [Presence] in Cervix by NAA with probe detection

0.00

-0.00

0.0

1.6

—

(3019060) Gas panel - Arterial blood

0.88

-0.00

32.3

4.3

—

(3002619) Bacteria identified in Specimen by Culture

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.9

—

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

0.00

-0.00

0.0

1.4

—

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

0.00

-0.00

0.0

2.4

—

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

0.00

-0.00

0.0

3.9

—

1.14

—

(3013566) Clostridioides difficile [Presence] in Stool by Organism specific culture

0.00

-0.00

0.0

1.0

—

(40758558) Short blood count panel - Blood

340

1.00

-0.00

4.5

6.9

—

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

Matched cohort

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints