This is a non-core endpoint: only basic statistics are computed.
Endpoint definition
↥
Endpoint definition steps |
FinnGen |
|---|---|
Phenotype data |
520210 |
1. Apply sex-specific ruleNone |
520210 |
2. Check conditionsNone |
520210 |
3. Check pre-conditions, main-only, mode, registry filtersRegistry filters:
2 out of 7 registries used, show all original rules. |
8 |
4. Check minimum number of eventsNone |
8 |
5. Include endpointsNone |
8 |
6. Filter based on genotype QC (FinnGen only) |
8 |
Control definitions (FinnGen only)
- Control exclude
- AB1_VIRAL_SKIN_MUCOUS_MEMBRANE
Extra metadata
- Level in the ICD hierarchy
- 3
- First used in FinnGen datafreeze
- DF5
Similar endpoints
↥List of similar endpoints to
Smallpox
based on the number of shared cases.
Similar with more cases:
- Viral infections characterized by skin and mucous membrane lesions
- Certain infectious and parasitic diseases
- Any operation in hilmo
- Any event in hilmo or specialist outpatient
- Any prescribed medicine buy
Similar with less cases:
None
Case counts by codes
↥FinnGen case counts by registry codes:
Not enough data for upset plot.
Not enough data for upset table.
Summary Statistics
↥-FinRegistry-
Key figures
| All | Female | Male | |
|---|---|---|---|
| Number of individuals | |||
| Whole population | 107 | 50 | 56 |
| Only index persons | 84 | 41 | 43 |
| 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 | 23.67 | 26.43 | 20.46 |
| Only index persons | 23.11 | 26.21 | 20.16 |
-FinnGen-
Key figures
| All | Female | Male | |
|---|---|---|---|
| Number of individuals | 8 | 5 | - |
| Unadjusted period prevalence (%) | 0.00 | 0.00 | - |
| Median age at first event (years) | 26.37 | 30.09 | - |
-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
↥OMOP Concept
People with measurements
Mean N measurements
Mean measured value
(ID) Name
N Cases
N Controls
OR
-log10(p)
cases
controls
unit
cases
controls
-log10(p)
N cases
N controls
(3029287) Urinalysis microscopic panel [#/volume] - Urine by Automated count
0
29
0.00
1.31
0.0
2.4
—
—
—
0
0
(3044640) Blood type and Crossmatch panel - Blood
0
26
0.00
1.01
0.0
2.9
—
—
—
0
0
(3002582) Erythrocytes [#/volume] in Urine
0
27
0.00
1.00
0.0
2.0
—
18.3
—
0
21
(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma
0
24
0.00
1.00
0.0
3.8
—
31.7
—
0
17
(3011397) Hemoglobin [Presence] in Urine by Test strip
0
21
0.00
0.72
0.0
4.7
—
—
—
0
0
(3030467) Casts [#/volume] in Urine by Automated count
0
21
0.00
0.72
0.0
2.0
—
0.1
—
0
15
(46236098) ABO and Rh group [Type] in Blood by Confirmatory method
0
18
0.00
0.70
0.0
3.3
—
—
—
0
0
(40758558) Short blood count panel - Blood
0
15
0.00
0.47
0.0
8.3
—
—
—
0
0
(3026008) Bacteria identified in Urine by Culture
0
15
0.00
0.47
0.0
2.5
—
—
—
0
0
(3030306) Epithelial cells.non-squamous [#/volume] in Urine by Automated count
0
15
0.00
0.47
0.0
1.9
—
0.7
—
0
9
(3029879) Epithelial cells.squamous [#/volume] in Urine by Automated count
0
14
0.00
0.46
0.0
2.0
—
3.3
—
0
8
(3003031) Transferrin.carbohydrate deficient.disialo/Transferrin.total in Serum or Plasma
0
11
0.00
0.23
0.0
1.7
—
1.7
—
0
11
(46235355) HIV 1 and 2 tests - Meaningful Use set
0
11
0.00
0.23
0.0
1.7
—
—
—
0
0
(3021879) Hepatitis B virus core Ab [Presence] in Serum
0
10
0.00
0.23
0.0
1.3
—
—
—
0
0
(3023368) Bacteria identified in Blood by Culture
0
12
0.00
0.23
0.0
5.3
—
—
—
0
0
(3017143) Hepatitis C virus Ab [Presence] in Serum
0
12
0.00
0.23
0.0
1.7
—
—
—
0
0
(3019284) Hepatitis B virus surface Ag [Presence] in Serum
0
13
0.00
0.22
0.0
1.6
—
—
—
0
0
(3019060) Gas panel - Arterial blood
0
8
0.00
0.00
0.0
2.9
—
—
—
0
0
(3002434) Lupus erythematosus deoxynucleoproteins IgG Ab [Units/volume] in Serum by Immunoassay
0
5
0.00
0.00
0.0
1.6
—
—
—
0
0
(36304997) Mycobacterium tuberculosis stimulated gamma interferon release by CD4+ and CD8+ T-cells [Units/volume] in Blood
0
6
0.00
0.00
0.0
1.3
—
—
—
0
0
(3000492) Spirometry study
0
5
0.00
0.00
0.0
1.6
—
—
—
0
0
(3004588) Protein electrophoresis panel - Serum or Plasma
0
7
0.00
0.00
0.0
1.0
—
—
—
0
0
(3028286) Albumin [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
37.7
—
0
5
(3008230) Borrelia burgdorferi IgM Ab [Units/volume] in Serum
0
6
0.00
0.00
0.0
2.3
—
—
—
0
0
(3006217) Methemoglobin/Hemoglobin.total in Arterial blood
0
6
0.00
0.00
0.0
3.8
—
0.8
—
0
6
(4035726)
0
7
0.00
0.00
0.0
1.6
—
—
—
0
0
(3015322) Alpha 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
2.9
—
0
5
(3005719) IgG [Mass/volume] in Serum or Plasma
0
6
0.00
0.00
0.0
4.0
—
8.5
—
0
6
(3030981) Hyaline casts [#/volume] in Urine by Automated count
0
6
0.00
0.00
0.0
2.0
—
0.0
—
0
6
(3029713) Protein.monoclonal band 1 [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
0.0
—
0
5
(3042936) Bacteria identified in Isolate by Culture
0
7
0.00
0.00
0.0
1.6
—
—
—
0
0
(3005229) Alpha 2 globulin [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
8.1
—
0
5
(3013742) Prealbumin [Mass/volume] in Serum or Plasma
0
6
0.00
0.00
0.0
2.0
—
0.2
—
0
6
(3035797) Protein.monoclonal band 2 [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
0.0
—
0
5
(3005785) Creatine kinase.MB [Mass/volume] in Serum or Plasma
0
7
0.00
0.00
0.0
2.7
—
8.0
—
0
7
(3007566) Smooth muscle Ab [Titer] in Serum
0
5
0.00
0.00
0.0
1.0
—
—
—
0
0
(3029338) Protein.monoclonal band 3 [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
0.0
—
0
5
(3014007) Fractional oxyhemoglobin in Arterial blood
0
5
0.00
0.00
0.0
4.2
—
94.7
—
0
5
(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
—
—
0
0
(36032419) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay
0
5
0.00
0.00
0.0
1.6
—
—
—
0
0
(3028026) IgM [Mass/volume] in Serum or Plasma
0
5
0.00
0.00
0.0
2.8
—
1.7
—
0
5
(3023465) Gamma globulin [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
11.5
—
0
5
(3029379) Protein.monoclonal band 4 [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
0.0
—
0
5
(3043747) Beta 2 globulin [Mass/volume] in Serum or Plasma by Electrophoresis
0
5
0.00
0.00
0.0
1.0
—
4.2
—
0
5
(3018405) Lactate [Moles/volume] in Arterial blood
0
5
0.00
0.00
0.0
4.0
—
1.3
—
0
5
(3025941) Bacteria identified in Stool by Culture
0
8
0.00
0.00
0.0
1.3
—
—
—
0
0
(3022621) pH of Urine by Test strip
0
7
0.00
0.00
0.0
1.4
—
—
—
0
0
(3020630) Protein [Mass/volume] in Serum or Plasma
0
9
0.00
0.00
0.0
1.1
—
66.8
—
0
9
(40761511) CBC panel - Blood by Automated count
8
73
+∞
0.00
8.6
13.4
—
—
—
0
0
(3017732) Neutrophils [#/volume] in Blood
0
7
0.00
0.00
0.0
3.7
—
2.7
—
0
7
(3012110) Lysozyme [Mass/volume] in Serum or Plasma
0
5
0.00
0.00
0.0
1.6
—
10.4
—
0
5
(3022250) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma by Lactate to pyruvate reaction
0
6
0.00
0.00
0.0
8.8
—
252.2
—
0
6
(3022145) Colonoscopy Study observation
0
6
0.00
0.00
0.0
1.3
—
—
—
0
0
(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood
0
6
0.00
0.00
0.0
3.8
—
1.9
—
0
6
(3024891) Influenza virus A+B Ag [Presence] in Specimen
0
5
0.00
0.00
0.0
1.0
—
—
—
0
0
(3034770) Mitochondria Ab [Titer] in Serum
0
5
0.00
0.00
0.0
1.0
—
—
—
0
0
(3004716) Salmonella sp identified in Stool by Organism specific culture
0
5
0.00
0.00
0.0
1.6
—
—
—
0
0
Mortality – FinRegistry
↥Association
Association between endpoint AB1_SMALLPOS and mortality.
Females
No dataMales
No dataMortality risk
Mortality risk for people of age
years, who have AB1_SMALLPOS.| 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_SMALLPOS – Smallpox
GWS hits: -
Endpoint
Case Overlap
Survival Analysis
Genetic Correlations
Genetic Signals
N (Jaccard index)
HR [CI]
Extremity
rg [CI]
Extremity
Hits
Coloc Hits
FinRegistry
FinnGen
FinRegistry
FinnGen
FinnGen
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