Esophageal ulcer

Summary

Esophageal ulcer (MONDO:0044782) is a disease with 19 GWAS associations across 9 studies and 1 clinical trial. A subtype of esophageal disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 19
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	esophageal ulcer
Mondo ID	MONDO:0044782
NCIT	C26950
UMLS	C0151970
MedGen	56254
Anatomy (UBERON)	UBERON:0001043
Is cancer (heuristic)	no

Also known as: esophageal ulcer · esophagus ulcer · esophagus ulcer disease · oesophagus ulcer · oesophagus ulcer disease · ulcer disease of esophagus · ulcer disease of oesophagus

Data availability: 19 GWAS associations (9 studies) · 1 HPO phenotype.

Disease family

This is a subtype of esophageal disorder. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease › human disease › disease by body system or component › digestive system disorder › upper digestive tract disorder › esophageal disorder › esophageal ulcer

Related subtypes (19): esophageal atresia, esophageal varices, esophagitis, megaesophagus, esophageal tuberculosis, esophageal leukoplakia, dyskinesia of esophagus, esophageal diverticulosis, gastroesophageal reflux disease, esophageal atresia/tracheoesophageal fistula, achalasia, Barrett esophagus, esophageal duplication cyst, tubular duplication of the esophagus, laryngotracheoesophageal cleft, isolated tracheo-esophageal fistula, congenital esophageal diverticulum, neoplasm of esophagus, congenital esophageal stenosis

Subtypes (1): peptic esophagitis

Genetics & variants

GWAS landscape

19 GWAS associations across 9 studies. Top hits map to 11 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs540106964	4e-14	PA2G4P3 - CDH2-AS1	G	2.97
rs183121790	1e-13	TECTA - TRPC6P5	G	2.76
rs190188858	3e-12	LINC00540	G	3.92
rs573908805	3e-12	LINC02315	G	2.85
rs543863390	5e-12	TRHDE	G	3.19
rs563013416	5e-12	ELF2P2 - FOXCUT	A	3.22
rs150556560	6e-12	YBX1 - CLDN19	G	2.76
rs919548295	8e-12	SOD2, WTAP	G	2.73
rs535597961	1e-11	GAPDHP56 - RNU6-224P	T	2.33
rs149697790	1e-11	SAMD5 - SASH1	G	4.38
rs142010700	2e-11	ATP6V1G1P7 - RPL7P45	A	4.55
rs541166768	2e-11	LINC01060	T	3.65
rs149284193	3e-11	SPATS2L	A	1.75
rs550175327	4e-11	TLN2 - TPM1-AS	G	3.54
rs566724933	4e-11	ALPK3	G	3.62
rs565099877	4e-11	ASIC2	C	2.86
rs144945290	4e-11	CLNK	G	2.64
rs184178719	3e-09	LINC02500 - TENM3-AS1	?
rs79286782	2e-08	CRLF1	?	1.22

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90432131	Jiang Y	2023	116,382	213,325	A cross-disorder study to identify causal relationships, shared genetic variants, and genes across 21 digestive disorders.
GCST90080189	Backman JD	2021	5,969	381,961	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084175	Backman JD	2021	5,969	381,961	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90436303	Zhou W	2018	5,243	369,275	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90478320	Verma A	2024	2,694	444,824	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651348	Liu TY	2025	621	195,643	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90480289	Verma A	2024	254	121,164	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90482131	Verma A	2024	254	121,164	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90482130	Verma A	2024	216	59,353	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	18

MAF distribution

Bucket	Variants
common (>=0.05)	1
low_freq (0.01-0.05)	0
rare (<0.01)	17
unknown	1

Functional consequences

Consequence	Count
intron_variant	12
intergenic_variant	6
regulatory_region_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs540106964	18	27901665	G>A	0.001	intergenic_variant	PA2G4P3 - CDH2-AS1	4e-14	Tier 4: intronic/intergenic
rs183121790	11	121229143	G>A	0.001	intergenic_variant	TECTA - TRPC6P5	1e-13	Tier 4: intronic/intergenic
rs190188858	13	22059970	G>T	0	intron_variant	LINC00540	3e-12	Tier 4: intronic/intergenic
rs573908805	14	41143799	G>T	0.001	intron_variant	LINC02315	3e-12	Tier 4: intronic/intergenic
rs543863390	12	72322949	G>A,T	0.001	intron_variant	TRHDE	5e-12	Tier 4: intronic/intergenic
rs563013416	6	1548612	A>T	0	intron_variant	ELF2P2 - FOXCUT	5e-12	Tier 4: intronic/intergenic
rs150556560	1	42717308	G>C,T	0.001	intergenic_variant	YBX1 - CLDN19	6e-12	Tier 4: intronic/intergenic
rs919548295	6	159740797	G>A,T	0.002	intron_variant	SOD2, WTAP	8e-12	Tier 4: intronic/intergenic
rs535597961	4	130688376	T>C	0.002	intergenic_variant	GAPDHP56 - RNU6-224P	1e-11	Tier 4: intronic/intergenic
rs149697790	6	148140038	G>T	0	intron_variant	SAMD5 - SASH1	1e-11	Tier 4: intronic/intergenic
rs142010700	13	104024766	A>C	0	regulatory_region_variant	ATP6V1G1P7 - RPL7P45	2e-11	Tier 3: regulatory
rs541166768	4	188415353	T>C	0.001	intergenic_variant	LINC01060	2e-11	Tier 4: intronic/intergenic
rs149284193	2	200420774	A>T	0.007	intron_variant	SPATS2L	3e-11	Tier 4: intronic/intergenic
rs550175327	15	62910191	G>A	0.002	intergenic_variant	TLN2 - TPM1-AS	4e-11	Tier 4: intronic/intergenic
rs566724933	15	84834752	G>T	0.002	intron_variant	ALPK3	4e-11	Tier 4: intronic/intergenic
rs565099877	17	33696785	C>A,T	0	intron_variant	ASIC2	4e-11	Tier 4: intronic/intergenic
rs144945290	4	10495800	G>A,C,T	0.001	intron_variant	CLNK	4e-11	Tier 4: intronic/intergenic
rs184178719	4	181680659	A>G		intron_variant	LINC02500 - TENM3-AS1	3e-09	Tier 4: intronic/intergenic
rs79286782	19	18605740	G>A,C,T	0.05	intron_variant	CRLF1	2e-08	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: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT03645070	Not specified	COMPLETED	Randomized Study on the Effect of Oesophageal Temperature on the Incidence of Esophageal Lesions After AF Ablation