eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| malt lymphoma | ||||
| Disease ID | 32 |
|---|---|
| Disease | malt lymphoma |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:5) |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:6) C0079731 | b-cell lymphoma | 18 C0009450 | infection | 10 C0024299 | lymphomas | 5 C0079731 | b-cell lymphomas | 2 C0079747 | low-grade lymphomas | 1 C0267373 | intestinal bleeding | 1 |
Manually Genotype(Total Text Mining Genotypes:0) |
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| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:42) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs1494555 | 20952689 | 7124 | TNF | umls:C0242647 | BeFree | After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for IFNGR2 (rs9808753 P(forinteraction) = .006), IL13 (rs20541 P(forinteraction) = .019), and IL7R (rs1494555 P(forinteraction) = .012) for marginal zone B-cell lymphoma; IL7R (rs1494555 P(forinteraction) = .017) for small lymphocytic lymphoma/chronic lymphocytic leukemia; and IL12A (rs568408 P(forinteraction) = .013) and TNF (1799724 P(forinteraction) = .04) for follicular lymphoma. | 0.005634266 | 2011 | IL7R | 5 | 35871088 | G | A |
| rs20541 | 20952689 | 7124 | TNF | umls:C0242647 | BeFree | After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for IFNGR2 (rs9808753 P(forinteraction) = .006), IL13 (rs20541 P(forinteraction) = .019), and IL7R (rs1494555 P(forinteraction) = .012) for marginal zone B-cell lymphoma; IL7R (rs1494555 P(forinteraction) = .017) for small lymphocytic lymphoma/chronic lymphocytic leukemia; and IL12A (rs568408 P(forinteraction) = .013) and TNF (1799724 P(forinteraction) = .04) for follicular lymphoma. | 0.005634266 | 2011 | IL13 | 5 | 132660272 | A | G |
| rs2922994 | 25569183 | 3106 | HLA-B | umls:C1367654 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.000271442 | 2014 | NA | 6 | 31368124 | A | G |
| rs2922994 | 25569183 | 56244 | BTNL2 | umls:C1367654 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.120271442 | 2014 | NA | 6 | 31368124 | A | G |
| rs2922994 | 25569183 | 3106 | HLA-B | umls:C0242647 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.000271442 | 2014 | NA | 6 | 31368124 | A | G |
| rs2922994 | 25569183 | 56244 | BTNL2 | umls:C0242647 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.120271442 | 2014 | NA | 6 | 31368124 | A | G |
| rs344550 | 22170086 | 347734 | SLC35B2 | umls:C0242647 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000814326 | 2012 | C3 | 19 | 6682942 | C | G |
| rs344550 | 22170086 | 714 | C1QC | umls:C1367654 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000271442 | 2012 | C3 | 19 | 6682942 | C | G |
| rs344550 | 22170086 | 714 | C1QC | umls:C0242647 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000271442 | 2012 | C3 | 19 | 6682942 | C | G |
| rs344550 | 22170086 | 347734 | SLC35B2 | umls:C1367654 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000271442 | 2012 | C3 | 19 | 6682942 | C | G |
| rs387906350 | NA | 8915 | BCL10 | umls:C0242647 | CLINVAR | NA | 0.149636822 | NA | BCL10 | 1 | 85267829 | - | A |
| rs387907272 | 25972321 | 4615 | MYD88 | umls:C1367654 | BeFree | The most distinguishing features of LPL with respect to MZL were focal paratrabecular involvement (P < .001), the presence of lymphoplasmacytoid cells (P < .001) and Dutcher bodies (P < .001), increased numbers of mast cells (P < .001), and the MYD88 L265P mutation (P < .001). | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 26230596 | 4615 | MYD88 | umls:C0242647 | BeFree | Thus, pyrosequencing for the MYD88 L265P mutation demonstrates a high clinical sensitivity and specificity to distinguish LPL from MZL and CLL. | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 25723115 | 4615 | MYD88 | umls:C1367654 | BeFree | MYD88 (L265P) somatic mutation in marginal zone B-cell lymphoma. | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 26230596 | 4615 | MYD88 | umls:C1367654 | BeFree | Thus, pyrosequencing for the MYD88 L265P mutation demonstrates a high clinical sensitivity and specificity to distinguish LPL from MZL and CLL. | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 25819228 | 4615 | MYD88 | umls:C1367654 | BeFree | MYD88 L265P was found in 49/51 (96%) LPL cases and in 1/13 (7·6%) MZL (splenic type), whereas all CLL samples remained negative. | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 22944768 | 4615 | MYD88 | umls:C1367654 | BeFree | IGHV gene features and MYD88 L265P mutation separate the three marginal zone lymphoma entities and Waldenström macroglobulinemia/lymphoplasmacytic lymphomas. | 0.001628651 | 2013 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 25819228 | 4615 | MYD88 | umls:C0242647 | BeFree | MYD88 L265P was found in 49/51 (96%) LPL cases and in 1/13 (7·6%) MZL (splenic type), whereas all CLL samples remained negative. | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 25723115 | 4615 | MYD88 | umls:C0242647 | BeFree | MYD88 (L265P) somatic mutation in marginal zone B-cell lymphoma. | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 25972321 | 4615 | MYD88 | umls:C0242647 | BeFree | The most distinguishing features of LPL with respect to MZL were focal paratrabecular involvement (P < .001), the presence of lymphoplasmacytoid cells (P < .001) and Dutcher bodies (P < .001), increased numbers of mast cells (P < .001), and the MYD88 L265P mutation (P < .001). | 0.001628651 | 2015 | MYD88 | 3 | 38141150 | T | C |
| rs387907272 | 22944768 | 4615 | MYD88 | umls:C0242647 | BeFree | IGHV gene features and MYD88 L265P mutation separate the three marginal zone lymphoma entities and Waldenström macroglobulinemia/lymphoplasmacytic lymphomas. | 0.001628651 | 2013 | MYD88 | 3 | 38141150 | T | C |
| rs497309 | 22170086 | 714 | C1QC | umls:C0242647 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000271442 | 2012 | C2 | 6 | 31924707 | A | C |
| rs497309 | 22170086 | 347734 | SLC35B2 | umls:C1367654 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000271442 | 2012 | C2 | 6 | 31924707 | A | C |
| rs497309 | 22170086 | 714 | C1QC | umls:C1367654 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000271442 | 2012 | C2 | 6 | 31924707 | A | C |
| rs497309 | 22170086 | 347734 | SLC35B2 | umls:C0242647 | BeFree | Additionally, SNPs (C2 rs497309, A>C and C3 rs344550, G>C) in two complement genes were positively associated with marginal zone lymphoma (MZL) and C1QG was associated with CLL/SLL, but these results were based on a limited number of cases. | 0.000814326 | 2012 | C2 | 6 | 31924707 | A | C |
| rs4986790 | 16971956 | 7099 | TLR4 | umls:C0242647 | BeFree | Furthermore, the TLR4 Asp299Gly variant was positively associated with the risk of mucosa-associated lymphoid tissue lymphoma (OR=2.76, 95% CI=1.12-6.81) and HL (OR=1.80, 95% CI=0.99-3.26). | 0.005634266 | 2006 | TLR4 | 9 | 117713024 | A | G |
| rs4986790 | 17086894 | 7099 | TLR4 | umls:C0242647 | BeFree | Genotyping for CD14 (-159C/T) and TLR4 (Asp 299Gly and Thr 399Ile) was performed in 70 patients with gastric mucosa-associated lymphoid tissue lymphoma (MALToma), 204 patients with non-cardia gastric adenocarcinoma (GAC), and 210 unrelated healthy controls. | 0.005634266 | 2006 | TLR4 | 9 | 117713024 | A | G |
| rs4986791 | 17086894 | 7099 | TLR4 | umls:C0242647 | BeFree | Genotyping for CD14 (-159C/T) and TLR4 (Asp 299Gly and Thr 399Ile) was performed in 70 patients with gastric mucosa-associated lymphoid tissue lymphoma (MALToma), 204 patients with non-cardia gastric adenocarcinoma (GAC), and 210 unrelated healthy controls. | 0.005634266 | 2006 | TLR4 | 9 | 117713324 | C | T |
| rs568408 | 20952689 | 7124 | TNF | umls:C0242647 | BeFree | After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for IFNGR2 (rs9808753 P(forinteraction) = .006), IL13 (rs20541 P(forinteraction) = .019), and IL7R (rs1494555 P(forinteraction) = .012) for marginal zone B-cell lymphoma; IL7R (rs1494555 P(forinteraction) = .017) for small lymphocytic lymphoma/chronic lymphocytic leukemia; and IL12A (rs568408 P(forinteraction) = .013) and TNF (1799724 P(forinteraction) = .04) for follicular lymphoma. | 0.005634266 | 2011 | IL12A;IL12A-AS1 | 3 | 159995680 | G | A |
| rs587776630 | NA | 8915 | BCL10 | umls:C0242647 | CLINVAR | NA | 0.149636822 | NA | BCL10 | 1 | 85270801 | - | T |
| rs587776631 | NA | 8915 | BCL10 | umls:C0242647 | CLINVAR | NA | 0.149636822 | NA | BCL10 | 1 | 85270619 | T | - |
| rs928883 | 22347493 | 406947 | MIR155 | umls:C1367654 | BeFree | Variant rs928883, near miR-155, showed an association (OR per A-allele: 2.80 [95% CI: 1.63-4.82]; p(F) = 0.027) with marginal zone lymphoma that is significant after correction for multiple testing. | 0.000271442 | 2012 | MIR155HG;LOC105372754 | 21 | 25571713 | A | G |
| rs928883 | 22347493 | 406947 | MIR155 | umls:C0242647 | BeFree | Variant rs928883, near miR-155, showed an association (OR per A-allele: 2.80 [95% CI: 1.63-4.82]; p(F) = 0.027) with marginal zone lymphoma that is significant after correction for multiple testing. | 0.000814326 | 2012 | MIR155HG;LOC105372754 | 21 | 25571713 | A | G |
| rs9461741 | 25569183 | 3106 | HLA-B | umls:C0242647 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.000271442 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9461741 | 25569183 | 3106 | HLA-B | umls:C1367654 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.000271442 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9461741 | 25569183 | 56244 | BTNL2 | umls:C0242647 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.120271442 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9461741 | 25569183 | 101929163 | LOC101929163 | umls:C0242647 | GWASCAT | A genome-wide association study of marginal zone lymphoma shows association to the HLA region. | 0.12 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9461741 | 25569183 | 56244 | BTNL2 | umls:C1367654 | GWASCAT | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.120271442 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9461741 | 25569183 | 56244 | BTNL2 | umls:C1367654 | BeFree | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.120271442 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9461741 | 25569183 | 56244 | BTNL2 | umls:C0242647 | GWASCAT | Here we perform a two-stage GWAS of 1,281 MZL cases and 7,127 controls of European ancestry and identify two independent loci near BTNL2 (rs9461741, P=3.95 × 10(-15)) and HLA-B (rs2922994, P=2.43 × 10(-9)) in the HLA region significantly associated with MZL risk. | 0.120271442 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9461741 | 25569183 | 101929163 | LOC101929163 | umls:C1367654 | GWASCAT | A genome-wide association study of marginal zone lymphoma shows association to the HLA region. | 0.12 | 2014 | BTNL2;LOC101929163 | 6 | 32402810 | G | C |
| rs9808753 | 20952689 | 7124 | TNF | umls:C0242647 | BeFree | After stratification by common B-cell lymphoma subtypes, a significant interaction was observed for IFNGR2 (rs9808753 P(forinteraction) = .006), IL13 (rs20541 P(forinteraction) = .019), and IL7R (rs1494555 P(forinteraction) = .012) for marginal zone B-cell lymphoma; IL7R (rs1494555 P(forinteraction) = .017) for small lymphocytic lymphoma/chronic lymphocytic leukemia; and IL12A (rs568408 P(forinteraction) = .013) and TNF (1799724 P(forinteraction) = .04) for follicular lymphoma. | 0.005634266 | 2011 | IFNGR2 | 21 | 33415005 | A | G |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
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| (Waiting for update.) | |
Mapped by lexical matching(Total Items:6) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000820 | Abnormality of the thyroid gland | MP:0020010 | decreased bone mineral density of femur | reduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh |
| HP:0012191 | B-cell lymphoma | MP:0009317 | increased follicular lymphoma incidence | higher than normal incidence of malignant lymphoma arising from lymphoid follicular B cells which may be small or large |
| HP:0000614 | Abnormality of the nasolacrimal system | MP:0009657 | failure of chorioallantoic fusion | failure to initiate and/or complete the formation of a highly vascularized extra-embryonic fetal membrane by fusion of the chorion and allantois |
| HP:0002017 | Nausea and vomiting | MP:0010426 | abnormal heart and great artery attachment | any anomaly in the in the position or pattern of the connection site of the heart to any of the great arteries, including the pulmonary artery and aorta |
| HP:0002205 | Recurrent respiratory infections | MP:0014182 | decreased respiratory epithelial sodium ion transmembrane transport | decrease in the directed movement of sodium ions from one side of the respiratory epithelial cell membrane to the other |
| HP:0001824 | Weight loss | MP:0005114 | premature hair loss | release of fur at an earlier than expected time |
Mapped by homologous gene(Total Items:17) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000975 | Hyperhidrosis | MP:0020187 | altered susceptibility to prion infection | altered likelihood that an organism will develop ill effects from the small proteinaceous infectious particles which are resistant to inactivation by procedures that modify nucleic acids and which contain an abnormal isoform of a cellular protein that is |
| HP:0001945 | Fever | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001824 | Weight loss | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0100721 | Mediastinal lymphadenopathy | MP:0014169 | decreased brown adipose tissue mass | decreased physical bulk or volume of brown adipose tissue |
| HP:0001903 | Anemia | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0012123 | Posterior uveitis | MP:0008079 | decreased CD8-positive, alpha-beta T cell number | reduction in the number of the regulatory subset of T lymphocytes that are involved in MHC class I restricted interactions |
| HP:0002027 | Abdominal pain | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0012191 | B-cell lymphoma | MP:0014082 | decreased small intestinal villus height | decreased height of the tiny hair-like projections which protrude from the inside of the small intestine and contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; usually accompanied by crypt elongation or hy |
| HP:0002716 | Lymphadenopathy | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0000505 | Visual impairment | MP:3000003 | abnormal Ebner's gland morphology | any structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l |
| HP:0002019 | Constipation | MP:0020234 | decreased basal metabolism | decrease in heat production of an organism at the lowest level of cell chemistry in an inactive, awake, and fasting state |
| HP:0000820 | Abnormality of the thyroid gland | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0002113 | Pulmonary infiltrates | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002205 | Recurrent respiratory infections | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0000614 | Abnormality of the nasolacrimal system | MP:0020039 | increased bone ossification | increase in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance |
| HP:0012378 | Fatigue | MP:0013659 | abnormal erythroid lineage cell morphology | any structural anomaly of an immature or mature cell in the lineage leading to and including erythrocytes |
| HP:0002017 | Nausea and vomiting | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| Disease ID | 32 |
|---|---|
| Disease | malt lymphoma |
| Case | (Waiting for update.) |