Lymphatic system cancer

Summary

Lymphatic system cancer (MONDO:0000612) is a cancer with 5 GWAS associations across 6 studies. A subtype of immune system cancer — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• GWAS associations: 5

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	lymphatic system cancer
Mondo ID	MONDO:0000612
DOID	DOID:0060073
Anatomy (UBERON)	UBERON:0006558
Is cancer (heuristic)	yes

Also known as: cancer of lymphatic part of lymphoid system · lymphatic part of lymphoid system cancer · malignant lymphatic part of lymphoid system neoplasm · malignant neoplasm of lymphatic part of lymphoid system

Data availability: 5 GWAS associations (6 studies).

Disease family

An umbrella term covering 4 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › cancer › immune system cancer › lymphatic system cancer

Related subtypes (24): T-cell childhood acute lymphocytic leukemia, B-cell childhood acute lymphoblastic leukemia, primary central nervous system lymphoma, thymus cancer, solitary plasmacytoma of chest wall, dendritic cell sarcoma, Waldeyer’s ring cancer, breast diffuse large B-cell lymphoma, colon Burkitt lymphoma, colorectal diffuse large B-cell lymphoma, gastric mantle cell lymphoma, liver diffuse large B-cell lymphoma, primary pulmonary diffuse large B-cell lymphoma, small intestinal Burkitt lymphoma, small intestinal diffuse large B-cell lymphoma, small intestinal enteropathy-associated T-cell lymphoma, thyroid gland diffuse large B-cell lymphoma, plasma cell myeloma, indolent primary cutaneous B-cell lymphoma, systemic Epstein-Barr virus-positive T-cell lymphoproliferative disease of childhood, mast cell sarcoma, subcutaneous panniculitis-like T-cell lymphoma, bone marrow cancer, primary vitreoretinal large b-cell lymphoma

Subtypes (4): lymph node cancer, lymphosarcoma, spleen cancer, reticulum cell sarcoma

Genetics & variants

GWAS landscape

5 GWAS associations across 6 studies. Top hits map to 1 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs2858314	8e-19	HLA-DQB1 - MTCO3P1	G	0.19
rs34087545	5e-14	HLA-DRB6 - HLA-DRB1	A	0.2
rs13255292	6e-12	PVT1	C	0.13
rs12365699	4e-11	Y_RNA - CXCR5	G	0.15
rs147193201	4e-09	IRF4 - EXOC2	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90475610	Verma A	2024	6,217	442,567	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435643	Zhou W	2018	2,270	404,466	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90477245	Verma A	2024	1,108	120,196	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479829	Verma A	2024	1,108	120,196	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651374	Liu TY	2025	875	235,192	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90477244	Verma A	2024	524	59,165	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	0
Tier 3: regulatory	1
Tier 4: intronic/intergenic	4

MAF distribution

Bucket	Variants
common (>=0.05)	5
low_freq (0.01-0.05)	0
rare (<0.01)	0
unknown	0

Functional consequences

Consequence	Count
intergenic_variant	3
intron_variant	1
regulatory_region_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs2858314	6	32695671	G>A,C	0.222	intergenic_variant	HLA-DQB1 - MTCO3P1	8e-19	Tier 4: intronic/intergenic
rs34087545	6	32575084	A>G	0.117	intergenic_variant	HLA-DRB6 - HLA-DRB1	5e-14	Tier 4: intronic/intergenic
rs13255292	8	128064327	C>T	0.267	intron_variant	PVT1	6e-12	Tier 4: intronic/intergenic
rs12365699	11	118872577	G>A	0.137	regulatory_region_variant	Y_RNA - CXCR5	4e-11	Tier 3: regulatory
rs147193201	6	484477	TCTAA>T,TCTAACTAA	0.05	intergenic_variant	IRF4 - EXOC2	4e-09	Tier 4: intronic/intergenic

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 0.