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	519972
1. Apply sex-specific rule None	519972
2. Check conditions None	519972
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.	107
4. Check minimum number of events None	107
5. Include endpoints None	107
6. Filter based on genotype QC (FinnGen only)	105

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	105	59	46
Unadjusted period prevalence (%)	0.02	0.02	0.02
Median age at first event (years)	61.48	57.61	66.44

-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
107: Matched controls
1070

Code

Vocabulary

Description

Odds Ratio

-log₁₀(p)

N matched cases

N matched controls

D13.5

ICD-10 Finland

Benign neoplasm: Extrahepatic bile ducts

+∞

141.3

102

JKA21

NOMESCO Finland

Laparoscopic cholecystectomy

11.8

37.2

D37.6

ICD-10 Finland

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

20.6

11.1

JJ1CE

NOMESCO Finland

Liver, bile duct and pancreas endoscopic ultrasound examination

109.3

9.6

K82.8

ICD-10 Finland

Other specified diseases of gallbladder

+∞

9.5

UJK02

NOMESCO Finland

ERCP

13.2

8.9

JN1AE

NOMESCO Finland

Ultrasound examination of upper part of abdomen

5.0

8.7

JKE98

NOMESCO Finland

Other transduodenal endoscopic operation on bile duct or ampulla of Vater

19.1

8.3

JN1CG

NOMESCO Finland

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

13.3

7.3

JL5SB

NOMESCO Finland

Endoscopic retrograd cholangiopancreaticography

15.6

6.5

R10.4

ICD-10 Finland

Other and unspecified abdominal pain

2.8

6.3

256

D37.7

ICD-10 Finland

Neoplasm of uncertain or unknown behaviour: Other digestive organs

9.5

6.2

JL5BG

NOMESCO Finland

MRI examinaiton of bile and pancreas ducts with high intesity magnet

13.6

6.2

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

107

4.19

9.97

2.2

4.5

2.85

12.30

ug/l

1.41

(3002256) Pathology report gross observation

3.26

5.78

1.3

—

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

407

2.33

4.37

2.4

2.3

—

(40768797) Stomach Pathology biopsy report

120

2.41

3.32

1.1

1.2

—

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

418

1.99

3.03

10.5

6.9

1.21

mmol/l

0.02

364

(3022948) Iron [Moles/volume] in Serum or Plasma

127

2.26

2.91

3.6

2.2

12.91

14.33

umol/l

0.46

117

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

5.27

2.77

1.3

1.6

2.14

6.84

u/ml

—

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

412

1.89

2.65

4.9

3.8

0.00

estimate

-0.00

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

104

2.27

2.58

1.5

—

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

5.70

2.58

1.8

1.2

—

(3034770) Mitochondria Ab [Titer] in Serum

3.68

2.55

1.3

1.2

—

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

419

1.84

2.46

4.9

3.7

0.00

estimate

-0.00

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

332

1.81

2.30

2.2

1.9

89.39

95.85

pmol/l

0.43

153

(3021589) Normoblasts [#/volume] in Blood

388

1.79

2.28

10.5

9.6

0.00

e9/l

-0.00

321

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

516

1.80

2.21

8.2

10.1

4.64

4.19

e9/l

0.76

451

(3001604) Monocytes [#/volume] in Blood

429

1.77

2.19

6.3

5.8

0.58

0.59

e9/l

0.13

381

(3006315) Basophils [#/volume] in Blood

430

1.76

2.16

6.3

5.8

0.05

0.04

e9/l

0.64

380

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

5.18

2.09

1.0

1.40

1.52

g/l

—

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

114

2.05

1.6

1.5

—

(3019198) Lymphocytes [#/volume] in Blood

436

1.72

2.01

6.3

5.8

1.83

1.89

e9/l

0.17

398

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

139

1.94

1.97

1.2

1.3

23.29

10.02

u/ml

0.25

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

188

1.83

1.94

2.9

1.9

3.19

3.17

mg/l

0.01

165

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

346

1.70

1.92

2.9

2.2

73.36

75.89

nmol/l

0.29

300

(3016251) Hemoglobin.gastrointestinal [Presence] in Stool

2.49

1.84

2.5

2.3

—

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

415

1.67

1.83

7.8

5.2

0.00

estimate

-0.00

(3013115) Eosinophils [#/volume] in Blood

445

1.66

1.80

6.5

6.1

0.23

0.18

e9/l

1.00

399

(40768804) Tissue Pathology biopsy report

354

1.65

1.72

2.6

2.0

—

(3048689) Calprotectin [Mass/mass] in Stool

100

1.96

1.65

2.3

1.9

126.38

164.89

ug/g

0.15

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

2.46

1.64

2.2

3.8

25.32

24.66

mmol/l

—

(3037467) Urinalysis macro (dipstick) panel - Urine

584

1.64

1.60

5.2

4.1

—

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

873

2.19

1.57

17.9

13.8

24.70

23.11

mg/l

0.15

669

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

2.54

1.57

1.3

2.2

—

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

2.70

1.54

1.4

1.1

—

(3041096) Erythrocytes [Presence] in Urine by Automated

246

1.63

1.48

5.2

3.4

—

(3049717) Cytology report of Urine Cyto stain

2.60

1.48

2.0

3.1

—

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

3.22

1.45

1.0

1.2

—

(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

2.29

1.45

1.2

1.8

—

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

2.70

1.39

1.3

1.1

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

2.01

1.35

1.1

1.3

—

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

190

1.64

1.35

2.4

2.2

—

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

148

1.71

1.34

1.3

11.63

36.25

iu/ml

—

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

108

1.80

1.32

20.8

6.8

105.11

104.00

mmol/l

0.38

108

(3000330) Specific gravity of Urine by Test strip

2.20

1.32

4.0

4.3

—

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

2.86

1.30

1.6

1.5

—

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

329

1.51

1.23

5.0

3.8

—

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

2.71

1.23

1.6

1.3

—

(40760892) CBC W Ordered Manual Differential panel - Blood

406

1.49

1.20

7.6

6.1

—

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

2.57

1.16

1.6

1.3

—

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

924

1.95

1.14

22.2

16.4

80.68

76.94

umol/l

0.45

924

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

1.92

1.14

3.8

3.3

54.40

59.42

ml/min/173m2

—

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

894

1.91

1.13

21.8

15.8

139.41

139.73

mmol/l

0.42

866

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

2.45

1.10

2.2

3.8

6.16

7.80

mmol/l

—

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

2.45

1.10

2.2

3.8

1.44

1.35

mmol/l

—

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

2.45

1.10

2.4

237.00

181.29

—

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

1.83

1.08

1.3

3.2

67.52

67.53

g/l

0.00

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

2.04

1.07

3.7

4.3

34.57

50.04

—

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

897

1.87

1.07

20.7

15.9

3.97

mmol/l

0.05

868

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

229

1.50

1.03

1.5

1.3

—

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

179

1.52

0.96

1.8

1.7

1.28

1.20

mg/l

0.04

139

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

251

1.46

0.95

6.5

2.9

0.39

0.54

e6/l

0.19

190

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

1.71

0.89

2.4

2.3

0.26

0.21

g/l

1.47

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

130

1.56

0.88

1.4

1.3

—

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

183

1.48

0.86

5.6

2.4

11.39

6.05

e6/l

0.36

166

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

157

1.51

0.85

4.0

2.8

3.85

1.16

e6/l

0.38

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

1.76

0.83

8.9

6.2

—

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

1.74

0.82

1.3

1.5

—

(3023368) Bacteria identified in Blood by Culture

230

1.42

0.82

4.7

4.0

—

(3022145) Colonoscopy Study observation

1.60

0.81

1.6

1.2

—

(3013139) Helicobacter pylori Ag [Presence] in Stool

1.76

0.78

1.6

1.3

—

(40768793) Breast Pathology biopsy report

2.23

0.77

1.4

1.2

—

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

161

1.46

0.76

3.3

3.1

2725.18

103.19

ng/l

0.46

128

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

1.69

0.76

28.8

7.2

0.64

0.66

—

(3044640) Blood type and Crossmatch panel - Blood

261

1.38

0.75

3.2

2.3

—

(3022217) INR in Platelet poor plasma by Coagulation assay

413

1.34

0.75

9.6

10.3

1.06

1.20

inr

0.68

119

(3004588) Protein electrophoresis panel - Serum or Plasma

1.74

0.75

1.1

3.1

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

1.66

0.74

28.8

7.1

1.11

1.72

—

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

1.97

0.71

1.6

1.1

—

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

1.97

0.71

1.4

1.1

—

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

1.89

0.69

1.0

1.3

—

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

1.89

0.69

3.8

6.3

—

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

1.89

0.69

1.0

1.3

—

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

1.89

0.69

1.0

1.3

—

(36304419) Bacteria [Presence] in Urine

246

1.37

0.69

6.5

2.8

—

(3002582) Erythrocytes [#/volume] in Urine

274

1.35

0.69

6.6

3.0

36.18

39.76

e6/l

0.05

215

(3000991) Gas panel - Venous blood

1.64

0.68

14.3

6.7

—

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

174

1.41

0.67

2.5

2.8

0.60

0.73

ug/l

0.83

115

(3007853) Bacteria identified in Skin by Aerobe culture

1.53

0.65

1.3

1.5

—

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

1.61

0.65

1.3

2.5

10.08

10.26

g/l

0.08

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

1.65

0.64

1.6

—

(3008898) HLA-B27 [Presence]

1.70

0.62

1.0

1.1

—

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

0.00

0.61

0.0

1.4

—

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

196

1.36

0.60

1.2

0.44

1.01

u/ml

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.60

0.0

1.8

—

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

347

1.29

0.59

3.4

4.0

33.28

33.30

ng/l

0.00

243

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

1.76

0.59

1.5

1.6

—

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

291

1.30

0.57

4.1

4.8

2.18

2.19

ug/l

0.00

255

(3018095) Leukocytes [#/volume] in Urine

310

1.30

0.57

7.7

3.5

59.24

64.38

e6/l

0.04

226

(3034780) Angiotensin converting enzyme [Enzymatic activity/volume] in Serum or Plasma

1.61

0.55

1.3

1.8

42.33

40.71

u/l

—

(3026782) Osmolality of Urine

172

1.35

0.54

5.6

3.1

567.41

544.45

mosm/kgh2o

0.16

148

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

101

1.44

0.53

1.7

—

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

101

1.44

0.53

1.6

—

(3020682) Albumin/Creatinine [Ratio] in Urine

275

1.29

0.52

4.4

3.5

6.92

11.14

mg/mmol

0.34

160

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

147

1.36

0.49

4.4

2.9

0.23

2.80

e6/l

2.22

(1761868) Lipid panel - Serum or Plasma

316

1.26

0.48

3.6

3.0

—

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

169

1.30

0.43

1.8

474.37

474.80

pmol/l

0.00

144

(3025941) Bacteria identified in Stool by Culture

1.41

0.42

1.6

1.2

—

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

106

1.37

0.41

8.5

7.5

—

(3004616) Nuclear Ab [Presence] in Serum

0.00

0.41

0.0

1.1

—

(3039443) Prostate specific Ag panel - Serum or Plasma

0.00

0.39

0.0

1.5

—

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

237

1.25

0.39

3.3

4.2

21.85

23.19

0.22

116

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

190

1.27

0.39

4.1

3.5

—

(3000492) Spirometry study

1.40

0.38

1.3

1.5

—

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

220

1.24

0.36

5.0

3.8

0.00

estimate

-0.00

(40761511) CBC panel - Blood by Automated count

915

1.34

0.36

18.6

12.8

—

(3013512) EKG study

249

1.23

0.36

4.2

3.9

—

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

1.38

0.35

1.5

1.8

—

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

1.32

0.33

1.2

200.13

161.20

u/ml

—

(3012516) Albumin [Mass/volume] in Urine

263

1.20

0.30

4.0

3.0

2426.37

72.63

mg/l

0.48

157

(3044889) 12 lead EKG panel

629

1.17

0.30

4.2

3.8

—

(40758558) Short blood count panel - Blood

226

1.20

0.28

5.0

7.9

—

(21494755) Public health laboratory ask at order entry panel

0.66

0.27

1.2

1.4

—

(4035726) Immunohistochemistry procedure

1.29

0.25

1.7

1.2

—

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

134

1.23

0.24

1.6

1.8

—

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

201

1.18

0.24

1.8

1.6

17.55

22.80

nmol/l

1.45

166

(3009542) Hematocrit [Volume Fraction] of Blood

968

1.30

0.22

30.0

20.5

39.57

40.15

0.39

901

(3000963) Hemoglobin [Mass/volume] in Blood

968

1.30

0.22

30.1

20.7

132.01

135.54

g/l

1.25

947

(3035941) MCH [Entitic mass]

968

1.30

0.22

29.6

20.4

30.14

30.38

0.64

947

(3024731) MCV [Entitic volume]

967

1.32

0.22

29.6

20.5

90.44

91.27

0.98

946

(3045142) Bone marrow Pathology biopsy report

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.2

—

(43055225) Phosphorylated tau 181 [Mass/volume] in Cerebral spinal fluid by Immunoassay

0.00

0.21

0.0

1.0

—

36.50

—

(4281824) Cell count and differential, peritoneal fluid

0.00

0.21

0.0

1.0

—

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

0.00

0.21

0.0

2.2

—

(3042810) Amyloid beta 42 peptide [Mass/volume] in Cerebral spinal fluid

0.00

0.21

0.0

1.0

—

485.00

—

(3000242) Tau protein [Mass/volume] in Cerebral spinal fluid

0.00

0.21

0.0

1.0

—

269.17

—

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

0.21

0.0

1.2

—

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

0.00

0.21

0.0

1.5

—

(3003181) Sodium [Moles/volume] in Urine

0.00

0.21

0.0

1.5

—

59.82

—

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

0.00

0.21

0.0

1.7

—

3.25

—

(3051651) Icteric interference index of Serum or Plasma

0.00

0.21

0.0

3.0

—

(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

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.21

0.0

1.4

—

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

0.00

0.21

0.0

1.8

—

13.58

—

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

1.29

0.21

1.3

1.6

—

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

1.29

0.21

1.5

1.3

—

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

0.00

0.21

0.0

2.5

—

3.39

—

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

0.00

0.21

0.0

1.2

—

(3051611) Lipemic interference index of Serum or Plasma

0.00

0.20

0.0

2.7

—

(3026008) Bacteria identified in Urine by Culture

262

1.15

0.20

2.2

3.0

—

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

1.19

0.20

1.0

—

(40761535) Cells panel - Urine sediment

1.15

0.17

2.1

2.8

—

(3019225) pH of Specimen

1.14

0.16

3.0

5.0

—

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

150

0.85

0.16

6.5

3.1

0.87

0.81

mmol/l

0.45

141

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

1.11

0.15

3.1

3.6

—

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

0.81

0.14

1.0

1.5

—

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

1.14

0.10

1.0

1.3

—

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

0.81

0.08

1.2

1.7

—

(3019060) Gas panel - Arterial blood

0.80

0.08

38.4

4.0

—

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

137

1.11

0.08

1.9

1.7

—

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

0.85

0.08

1.7

1.8

—

(40761536) Microorganisms panel - Urine sediment

0.82

0.08

10.3

3.4

—

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

0.80

0.08

1.3

1.7

—

(3000494) Fungus identified in Specimen by Culture

112

0.88

0.07

1.0

1.4

—

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

526

0.94

0.07

2.8

2.9

—

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

827

1.07

0.06

18.7

13.4

80.86

80.76

ml/min/173m2

0.01

664

(3042936) Bacteria identified in Isolate by Culture

131

1.08

0.04

2.6

1.8

—

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

133

1.06

0.01

1.4

1.3

—

(36660697) Celiac disease serology panel - Serum

0.95

0.00

1.0

1.1

—

(3011831) Apolipoprotein B/Apolipoprotein A-I [Percentile]

0.00

-0.00

0.0

1.8

—

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

0.00

-0.00

0.0

1.2

—

(3047189) Immunofixation for 24 hour Urine

0.00

-0.00

0.0

1.9

—

(3051593) INR in Capillary blood by Coagulation assay

0.00

-0.00

0.0

13.8

—

(4146454) Self-monitoring of blood glucose

0.00

-0.00

0.0

2.3

—

(3017704) Immunofixation for Urine

0.00

-0.00

0.0

1.7

—

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

0.00

-0.00

0.0

3.9

—

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

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

6.6

—

231.20

—

(4200892) Spirometry reversibility

0.98

-0.00

1.3

1.4

—

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

0.00

-0.00

0.0

2.1

—

19.24

—

(3008364) Apolipoprotein A-I [Mass/volume] in Serum or Plasma

0.00

-0.00

0.0

1.8

—

1.47

—

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

0.00

-0.00

0.0

19.0

—

1544.00

—

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

0.00

-0.00

0.0

4.3

—

(3007798) IgG/Albumin [Mass Ratio] in Cerebral spinal fluid

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

1.7

—

1.21

—

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

0.00

-0.00

0.0

1.1

—

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

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.8

—

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

0.00

-0.00

0.0

1.5

—

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

0.00

-0.00

0.0

1.4

—

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

0.00

-0.00

0.0

1.0

—

144.78

—

(3038297) Parainfluenza virus 4 RNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

2.2

—

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

0.88

-0.00

1.7

2.0

1.64

5.05

ug/l

—

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

0.00

-0.00

0.0

1.0

—

(3036432) Mycobacterium tuberculosis genotype [Identifier] in Isolate

0.00

-0.00

0.0

9.8

—

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

0.00

-0.00

0.0

2.0

—

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

0.00

-0.00

0.0

14.2

—

881.83

—

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

0.00

-0.00

0.0

1.2

—

11.40

—

(3005156) Respiratory syncytial virus A RNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

2.4

—

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

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.4

—

(3024263) Appearance of Synovial fluid

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.6

—

63.20

—

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

0.00

-0.00

0.0

1.6

—

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

0.00

-0.00

0.0

2.3

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.94

-0.00

1.8

1.7

—

(3004451) EKG impression Narrative

0.00

-0.00

0.0

1.8

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

-0.00

0.0

1.2

—

(3002619) Bacteria identified in Specimen by Culture

0.00

-0.00

0.0

1.0

—

(3000108) Respiratory syncytial virus B RNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

2.4

—

(21493195) Respiratory pathogens DNA and RNA tested for in Respiratory system specimen by NAA with probe detection

0.00

-0.00

0.0

2.4

—

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

0.00

-0.00

0.0

1.5

—

73.17

—

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

0.00

-0.00

0.0

1.6

—

(3023511) Choriogonadotropin [Units/volume] in Urine

0.00

-0.00

0.0

1.6

—

(3029075) Extractable nuclear Ab panel - Serum

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.2

—

(3005033) Fetal Nuchal fold Thickness US

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.0

—

183.56

—

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

0.00

-0.00

0.0

1.5

—

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

0.00

-0.00

0.0

4.3

—

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

0.00

-0.00

0.0

2.3

—

(3025634) Parainfluenza virus 1 RNA [Presence] in Specimen by NAA with probe detection

0.00

-0.00

0.0

2.2

—

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

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.0

—

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

0.00

-0.00

0.0

1.2

—

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

0.00

-0.00

0.0

1.6

—

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

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

1.6

—

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

0.00

-0.00

0.0

1.3

—

33.73

—

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