chr2:113590390:G>A Detail (hg19) (IL1B)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:113,590,390-113,590,390 |
| hg38 | chr2:112,832,813-112,832,813 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000576.2:c.315C>T | NP_000567.1:p.Phe105= |
| Ensemble | ENST00000263341.7:c.315C>T | ENST00000263341.7:p.Phe105= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.036 |
| ToMMo:0.048 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.022 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
association
|
2020-02-10 | no assertion criteria provided | antisynthetase syndrome |
germline
|
Detail |
Affects
|
2021-10-20 | no assertion criteria provided | endometriosis |
somatic
|
Detail |
other
|
2022-12-10 | no assertion criteria provided | cholangiocarcinoma |
germline
|
Detail |
|
Benign
|
2019-11-19 | criteria provided, single submitter | IL1B-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.001 | colorectal carcinoma | We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634... | BeFree | 23192617 | Detail |
| 0.003 | Migraine Disorders | In this study, the association of the occurrence and clinical characteristics of... | BeFree | 20113413 | Detail |
| <0.001 | Carcinoma of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| 0.006 | colorectal carcinoma | We found that rs1143634 in the interleukin-1β (IL1B) gene and rs1800871 in the i... | BeFree | 24557062 | Detail |
| 0.044 | Malignant neoplasm of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| 0.005 | Atopy | [We conclude that the IL1a*1/IL1B*1/IL1RN*2 haplotype contains the decisive alla... | GAD | 12746420 | Detail |
| 0.001 | Osteoarthritis of hip | The meta-analysis of six published studies retrieved from the literature search ... | BeFree | 21146623 | Detail |
| 0.010 | Gingival Diseases | We investigated associations between three IL1 single-nucleotide polymorphisms (... | BeFree | 24460370 | Detail |
| 0.013 | colorectal cancer | We found that rs1143634 in the interleukin-1β (IL1B) gene and rs1800871 in the i... | BeFree | 24557062 | Detail |
| <0.001 | Carcinoma of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| 0.080 | Diabetes | The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher gl... | BeFree | 19820020 | Detail |
| 0.005 | Carcinoma of lung | IL1B rs1143634 polymorphism, cigarette smoking, alcohol use, and lung cancer ris... | BeFree | 20035239 | Detail |
| 0.005 | Carcinoma of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| 0.044 | Malignant neoplasm of lung | [IL1B rs1143634 polymorphism, cigarette smoking, alcohol use, and lung cancer ri... | GAD | 20035239 | Detail |
| 0.029 | Periodontal Diseases | We investigated associations between three IL1 single-nucleotide polymorphisms (... | BeFree | 24460370 | Detail |
| 0.026 | Degenerative polyarthritis | Haplotype analyses revealed gender disparities and showed that women carriers of... | BeFree | 23216199 | Detail |
| 0.139 | Migraine Disorders | In this study, the association of the occurrence and clinical characteristics of... | BeFree | 20113413 | Detail |
| 0.018 | Malignant neoplasm of prostate | [Using Multivariate Adaptive Regression Splines modeling for exploratory SNP-SNP... | GAD | 19474090 | Detail |
| 0.008 | Malignant neoplasm of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| 0.005 | Malignant neoplasm of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| <0.001 | diabetes mellitus | The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher gl... | BeFree | 19820020 | Detail |
| 0.044 | Malignant neoplasm of lung | IL1B rs1143634 polymorphism, cigarette smoking, alcohol use, and lung cancer ris... | BeFree | 20035239 | Detail |
| <0.001 | Carcinoma of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| <0.001 | Diabetes | The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher gl... | BeFree | 19820020 | Detail |
| 0.022 | ankylosing spondylitis | Polymorphisms of IL1α rs1800587, IL1β rs16944 and IL1β rs1143634 were not signif... | BeFree | 22285486 | Detail |
| 0.015 | ankylosing spondylitis | Polymorphisms of IL1α rs1800587, IL1β rs16944 and IL1β rs1143634 were not signif... | BeFree | 22285486 | Detail |
| 0.010 | Malignant neoplasm of lung | CART analyses did not yield a tree structure for overall survival; separate CART... | BeFree | 25597281 | Detail |
| 0.295 | diabetes mellitus | The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher gl... | BeFree | 19820020 | Detail |
| 0.006 | colorectal cancer | We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634... | BeFree | 23192617 | Detail |
| 0.023 | ankylosing spondylitis | This study's purpose is to investigate the association of ankylosing spondylitis... | BeFree | 22285486 | Detail |
| 0.082 | Lung diseases | SNPs rs1143634 and rs1143639 in the IL1B gene demonstrated a consistent associat... | BeFree | 19431193 | Detail |
| 0.020 | HIV Infections | The 2 polymorphisms rs10754558 in NLRP3 and rs1143634 in IL1B were significantly... | BeFree | 22227487 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000576.3(IL1B):c.315C>T (p.Phe105=) AND Antisynthetase syndrome | ClinVar | Detail |
| NM_000576.3(IL1B):c.315C>T (p.Phe105=) AND Endometriosis | ClinVar | Detail |
| NM_000576.3(IL1B):c.315C>T (p.Phe105=) AND Cholangiocarcinoma | ClinVar | Detail |
| NM_000576.3(IL1B):c.315C>T (p.Phe105=) AND IL1B-related disorder | ClinVar | Detail |
| We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634) and IL1-RN +2018T&... | DisGeNET | Detail |
| In this study, the association of the occurrence and clinical characteristics of migraine with the p... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| We found that rs1143634 in the interleukin-1β (IL1B) gene and rs1800871 in the interleukin-10 (IL10)... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| [We conclude that the IL1a*1/IL1B*1/IL1RN*2 haplotype contains the decisive allale or allele combina... | DisGeNET | Detail |
| The meta-analysis of six published studies retrieved from the literature search and eight unpublishe... | DisGeNET | Detail |
| We investigated associations between three IL1 single-nucleotide polymorphisms (SNPs) in genes encod... | DisGeNET | Detail |
| We found that rs1143634 in the interleukin-1β (IL1B) gene and rs1800871 in the interleukin-10 (IL10)... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher glucose, higher homeos... | DisGeNET | Detail |
| IL1B rs1143634 polymorphism, cigarette smoking, alcohol use, and lung cancer risk in a Japanese popu... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| [IL1B rs1143634 polymorphism, cigarette smoking, alcohol use, and lung cancer risk in a Japanese pop... | DisGeNET | Detail |
| We investigated associations between three IL1 single-nucleotide polymorphisms (SNPs) in genes encod... | DisGeNET | Detail |
| Haplotype analyses revealed gender disparities and showed that women carriers of the 1-2-1-1 haploty... | DisGeNET | Detail |
| In this study, the association of the occurrence and clinical characteristics of migraine with the p... | DisGeNET | Detail |
| [Using Multivariate Adaptive Regression Splines modeling for exploratory SNP-SNP interactions, our r... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher glucose, higher homeos... | DisGeNET | Detail |
| IL1B rs1143634 polymorphism, cigarette smoking, alcohol use, and lung cancer risk in a Japanese popu... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher glucose, higher homeos... | DisGeNET | Detail |
| Polymorphisms of IL1α rs1800587, IL1β rs16944 and IL1β rs1143634 were not significantly associated w... | DisGeNET | Detail |
| Polymorphisms of IL1α rs1800587, IL1β rs16944 and IL1β rs1143634 were not significantly associated w... | DisGeNET | Detail |
| CART analyses did not yield a tree structure for overall survival; separate CART tree structures wer... | DisGeNET | Detail |
| The haplotype ACG of rs1143634, rs3917356, and rs16944 associated with higher glucose, higher homeos... | DisGeNET | Detail |
| We investigated whether IL-1B -511C>T (rs16944), IL-1B +3954C>T (rs1143634) and IL1-RN +2018T&... | DisGeNET | Detail |
| This study's purpose is to investigate the association of ankylosing spondylitis with single-nucleot... | DisGeNET | Detail |
| SNPs rs1143634 and rs1143639 in the IL1B gene demonstrated a consistent association with lung diseas... | DisGeNET | Detail |
| The 2 polymorphisms rs10754558 in NLRP3 and rs1143634 in IL1B were significantly associated to the H... | DisGeNET | Detail |
Overlapped Transcript Coordinates
| Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
|---|
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs1143634 dbSNP
- Genome
- hg19
- Position
- chr2:113,590,390-113,590,390
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- A
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1190
- Mean of sample read depth (HGVD)
- 80.61
- Standard deviation of sample read depth (HGVD)
- 33.27
- Number of reference allele (HGVD)
- 2295
- Number of alternative allele (HGVD)
- 85
- Allele Frequency (HGVD)
- 0.03571428571428571
- Gene Symbol (HGVD)
- IL1B
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs1143634
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.048
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 805
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 192
- East Asian Heterozygous Counts (ExAC)
- 188
- East Asian Homozygous Counts (ExAC)
- 2
- East Asian Allele Frequency (ExAC)
- 0.022186272244048996
- Chromosome Counts in All Race (ExAC)
- 121404
- Allele Counts in All Race (ExAC)
- 23848
- Heterozygous Counts in All Race (ExAC)
- 18552
- Homozygous Counts in All Race (ExAC)
- 2648
- Allele Frequency in All Race (ExAC)
- 0.1964350433264143
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