Risteys · AB1_CHLAMYDIA

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 — A55 Hospital discharge: ICD-9 — 0991A Hospital discharge: ICD-8 — 0991A Cause of death: ICD-10 — A55 Cause of death: ICD-9 — 0991A Cause of death: ICD-8 — 0991A 2 out of 7 registries used, show all original rules.	25
4. Check minimum number of events None	25
5. Include endpoints None	25
6. Filter based on genotype QC (FinnGen only)	25

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	76	10	64
Only index persons	68	9	59
Unadjusted period prevalence (%)
Whole population	0.00	0.00	0.00
Only index persons	0.00	0.00	0.00
Median age at first event (years)
Whole population	46.90	63.46	44.56
Only index persons	45.87	61.42	43.49

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	25	-	23
Unadjusted period prevalence (%)	0.01	-	0.01
Median age at first event (years)	44.31	-	44.16

-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

No data

-FinnGen-

Cumulative Incidence Function

Not a core endpoint, no data to show.

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.

No data available

LabWAS

↥

(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3006093) Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection

150.42

20.06

13.6

2.3

—

(3011371) Neisseria gonorrhoeae DNA [Presence] in Specimen by NAA with probe detection

129.22

19.48

13.2

2.0

—

(3029634) Reagin Ab [Titer] in Serum by VDRL

143.73

19.16

18.0

3.8

6.7

—

titre

—

(3019832) Treponema pallidum Ab [Presence] in Serum

65.74

16.11

3.4

1.8

—

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

23.82

10.73

5.8

2.3

—

(40758558) Short blood count panel - Blood

15.45

8.71

14.1

8.3

—

(42870588) Differential panel, method unspecified - Blood

12.82

7.74

13.7

6.6

—

(3033658) Prothrombin time (PT) actual/Normal

9.83

6.55

3.2

3.6

92.4

92.0

0.02

(3013762) Body weight Measured

+∞

6.51

1.2

0.0

—

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

9.79

6.47

3.0

5.6

—

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

7.88

6.20

1.9

1.5

1.2

1.6

mmol/l

1.63

(3018095) Leukocytes [#/volume] in Urine

8.62

5.92

4.5

2.9

16.0

7.3

e6/l

—

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

6.44

4.99

8.5

1.9

—

(3015736) pH of Urine

6.82

4.94

2.9

4.4

—

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

12.58

3.70

3.0

1.2

—

(36304419) Bacteria [Presence] in Urine

4.21

2.97

2.9

2.1

—

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

6.48

2.97

1.3

—

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

4.61

2.73

1.4

1.5

—

(3011288) Drugs identified in Urine by Screen method

7.45

2.49

3.0

1.3

—

(40768804) Tissue Pathology biopsy report

3.69

2.49

2.9

1.7

—

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

3.76

2.48

3.2

4.0

—

0.0

—

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

6.61

2.33

6.0

1.2

—

(3013826) Glucose [Moles/volume] in Serum or Plasma

100

3.17

2.00

7.5

5.5

5.8

6.7

mmol/l

2.41

(3012544) pH of Venous blood

4.91

1.92

2.4

6.2

—

(3007853) Bacteria identified in Skin by Aerobe culture

4.04

1.87

1.3

1.7

—

(3021447) Carbon dioxide [Partial pressure] in Venous blood

4.52

1.81

2.4

5.8

5.7

6.1

kpa

—

(3002256) Pathology report gross observation

4.18

1.70

1.4

1.1

—

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

2.80

1.62

3.0

—

(3000494) Fungus identified in Specimen by Culture

3.25

1.54

1.5

—

(3029187) Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma

0.00

1.49

0.0

4.6

—

706.3

—

(1761868) Lipid panel - Serum or Plasma

105

0.35

1.47

2.0

2.4

—

(3026910) Gamma glutamyl transferase [Enzymatic activity/volume] in Serum or Plasma

177

0.38

1.47

3.2

3.0

71.3

43.1

u/l

0.37

171

(3023368) Bacteria identified in Blood by Culture

2.78

1.40

7.3

4.3

—

(3042936) Bacteria identified in Isolate by Culture

2.83

1.33

2.2

2.4

—

(3000492) Spirometry study

0.00

1.27

0.0

1.4

—

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

2.73

1.22

2.1

2.3

—

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

2.23

1.04

1.3

1.5

—

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

2.49

0.99

1.7

1.8

34.0

37.2

nmol/l

—

(3044640) Blood type and Crossmatch panel - Blood

1.97

0.72

2.4

2.3

—

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

0.00

0.61

0.0

1.1

—

(40761511) CBC panel - Blood by Automated count

216

0.63

0.43

9.4

9.3

—

(40761535) Cells panel - Urine sediment

0.00

0.42

0.0

5.2

—

(3021440) Promyelocytes/100 leukocytes in Blood

0.00

0.42

0.0

5.6

—

1.0

—

(3017181) Myelocytes/100 leukocytes in Blood

0.00

0.41

0.0

5.5

—

1.5

—

(3018418) pH of Serum or Plasma

1.65

0.40

3.0

6.8

—

7.4

—

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

1.37

0.32

7.6

8.7

1.2

mmol/l

—

(3044889) 12 lead EKG panel

123

0.69

0.30

2.0

3.1

—

(3022313) Gas panel - Capillary blood

0.00

0.22

0.0

1.4

—

(40761536) Microorganisms panel - Urine sediment

0.00

0.22

0.0

2.1

—

(3027238) Thyroperoxidase Ab [Units/volume] in Serum or Plasma

0.00

0.21

0.0

1.1

—

127.0

—

(3026493) Urate [Moles/volume] in Serum or Plasma

1.23

0.21

2.5

3.3

346.7

9270.2

umol/l

—

(3009343) pH of Capillary blood

0.00

0.21

0.0

1.4

—

(3023024) Carbon dioxide [Partial pressure] in Capillary blood

0.00

0.21

0.0

1.4

—

5.1

—

(3032080) INR in Blood by Coagulation assay

1.23

0.20

2.3

5.6

—

1.2

—

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

186

1.37

0.20

15.5

13.1

139.1

139.8

mmol/l

0.48

180

(3009508) Creatinine [Moles/volume] in Urine

1.20

0.11

4.2

3.0

9.3

10.1

mmol/l

—

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

191

1.23

0.09

16.0

13.0

3.9

4.0

mmol/l

1.59

185

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

1.14

0.09

2.4

4.1

—

(3019060) Gas panel - Arterial blood

0.00

0.0

5.1

—

(3048816) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Blood

0.00

0.0

3.8

—

1.2

—

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

0.00

0.0

7.7

—

25.6

—

(4034850)

0.00

0.0

13.3

—

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

0.00

0.0

5.3

—

58.5

—

(42868544) Hantavirus puumala IgM Ab [Presence] in Serum or Plasma by Immunofluorescence

0.00

0.0

1.2

—

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

0.00

0.0

2.3

—

(3014148) Varicella zoster virus Ab [Titer] in Serum

0.00

0.0

1.0

—

(3030981) Hyaline casts [#/volume] in Urine by Automated count

0.00

0.0

3.7

—

0.1

—

(3020891) Body temperature

0.00

0.0

7.6

—

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

0.00

0.0

2.2

—

3.4

—

(3015816) F5 gene p.Arg506Gln [Presence] in Blood or Tissue by Molecular genetics method

0.00

0.0

1.0

—

(3026989) Triiodothyronine (T3) Free [Moles/volume] in Serum or Plasma

0.00

0.0

3.5

—

4.5

—

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

0.00

0.0

16.8

—

977.3

—

(3020287) Protein C actual/normal in Platelet poor plasma by Coagulation assay

0.00

0.0

1.0

—

105.8

—

(3018405) Lactate [Moles/volume] in Arterial blood

0.00

0.0

5.1

—

1.5

—

(4094501)

0.00

0.0

1.0

—

(3020629) Protein S Free Ag actual/normal in Platelet poor plasma by Immunoassay

0.00

0.0

1.0

—

83.8

—

(3023150) Myeloperoxidase Ab [Units/volume] in Serum

0.00

0.0

1.0

—

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

0.00

0.0

2.4

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.0

7.4

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.0

—

(4306422)

0.00

0.0

1.0

—

(3000330) Specific gravity of Urine by Test strip

0.00

0.0

2.3

—

(3004119) Hemoglobin [Mass/volume] in Venous blood

0.00

0.0

4.6

—

121.6

—

(3010517) Carboxyhemoglobin/Hemoglobin.total in Venous blood

0.00

0.0

4.4

—

1.8

—

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

0.00

0.0

2.0

—

(3012220) Varicella zoster virus IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.1

—

(3002482) Mycoplasma pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.3

—

(3016881) Enterovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.6

—

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

0.00

0.0

2.3

—

(3012447) Hantavirus puumala IgG Ab [Titer] in Serum

0.00

0.0

1.0

—

(3046279) Procalcitonin [Mass/volume] in Serum or Plasma

0.00

0.0

2.4

—

0.4

—

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

0.00

0.0

2.7

—

(3005895) Myoglobin [Mass/volume] in Serum or Plasma

0.00

0.0

1.8

—

240.4

—

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

0.00

0.0

2.7

—

Mortality – FinRegistry

↥

Association

Association between endpoint AB1_CHLAMYDIA_VENERUM and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have AB1_CHLAMYDIA_VENERUM.

N-year risk	Females	Males
1	No data	No data
5	No data	No data
10	No data	No data
15	No data	No data
20	No data	No data

Relationships between endpoints

↥

Index endpoint: AB1_CHLAMYDIA_VENERUM – Chlamydial lymphogranuloma (venereum)

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

NAME	AB1_CHLAMYDIA_VENERUM
CONTROL_EXCLUDE	AB1_SEXUAL_TRANSMISSION
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	A55
HD_ICD_9	0991A
HD_ICD_8	0991A
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	A55
COD_ICD_9	0991A
COD_ICD_8	0991A
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

Chlamydial lymphogranuloma (venereum)

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)

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints