IRX1

Summary

IRX1 (iroquois homeobox 1, HGNC:14358) is a protein-coding gene on chromosome 5p15.33, encoding Iroquois-class homeodomain protein IRX-1 (P78414).

This gene encodes a member of the Iroquois homeobox protein family. Homeobox genes in this family are involved in pattern formation in the embryo. The gene product has been identified as a tumor suppressor in gastric (PMID: 21602894, 20440264) and head and neck cancers (PMID: 18559491). A pseudogene of this gene is located on chromosome 13.

Source: NCBI Gene 79192 — RefSeq curated summary.

At a glance

• GWAS associations: 24
• Clinical variants (ClinVar): 102 total — 2 pathogenic
• Transcription factor: yes — 20 downstream targets (CollecTRI)
• MANE Select transcript: NM_024337

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14358
Approved symbol	IRX1
Name	iroquois homeobox 1
Location	5p15.33
Locus type	gene with protein product
Status	Approved
Aliases	IRX-5
Ensembl gene	ENSG00000170549
Ensembl biotype	protein_coding
OMIM	606197
Entrez	79192

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000302006

RefSeq mRNA: 1 — MANE Select: NM_024337 NM_024337

CCDS: CCDS34132

Canonical transcript exons

ENST00000302006 — 4 exons

Exon	Start	End
ENSE00001169542	3600609	3600681
ENSE00001169552	3599225	3600260
ENSE00001196749	3600983	3601403
ENSE00001290275	3595832	3596381

Expression profiles

Bgee: expression breadth ubiquitous, 140 present calls, max score 90.68.

FANTOM5 (CAGE): breadth broad, TPM avg 4.3549 / max 281.1696, expressed in 571 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
55606	1.7038	464
55604	1.4657	460
55605	0.8961	375
55608	0.1946	115
55607	0.0948	43

Top tissues by expression

232 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	90.68	gold quality
epithelium of mammary gland	UBERON:0003244	90.30	gold quality
mammary duct	UBERON:0001765	90.25	gold quality
renal medulla	UBERON:0000362	87.67	gold quality
mammary gland	UBERON:0001911	86.64	gold quality
thoracic mammary gland	UBERON:0005200	86.52	gold quality
metanephros cortex	UBERON:0010533	83.57	gold quality
upper arm skin	UBERON:0004263	82.89	silver quality
saliva-secreting gland	UBERON:0001044	80.13	gold quality
metanephros	UBERON:0000081	79.72	gold quality
minor salivary gland	UBERON:0001830	79.06	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.15	gold quality
kidney epithelium	UBERON:0004819	78.01	gold quality
adult mammalian kidney	UBERON:0000082	77.39	gold quality
mouth mucosa	UBERON:0003729	77.10	gold quality
skin of leg	UBERON:0001511	75.73	gold quality
subcutaneous adipose tissue	UBERON:0002190	75.13	gold quality
zone of skin	UBERON:0000014	74.76	gold quality
skin of hip	UBERON:0001554	74.56	gold quality
parietal pleura	UBERON:0002400	73.85	gold quality
kidney	UBERON:0002113	73.41	gold quality
pons	UBERON:0000988	73.06	gold quality
skin of abdomen	UBERON:0001416	72.67	gold quality
upper leg skin	UBERON:0004262	72.07	gold quality
nipple	UBERON:0002030	70.68	gold quality
right lung	UBERON:0002167	68.77	gold quality
gingiva	UBERON:0001828	68.25	gold quality
hypothalamus	UBERON:0001898	67.98	gold quality
gingival epithelium	UBERON:0001949	67.41	silver quality
lower lobe of lung	UBERON:0008949	67.09	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.49

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

20 targets.

Target	Regulation
ANPEP	Activation
BDKRB2	Repression
BPI	Repression
CELF2	Repression
COL9A3	Repression
DKK3	Repression
EGR1	Repression
ERMAP	Activation
FGF7	Repression
INHBA	Activation
IRX1
KDR	Activation
NPTX1	Repression
PHYHIPL	Repression
PTGER1	Repression
PTGS2	Activation
RALGPS1	Activation
SHH	Unknown
SPON1	Activation
UGT8	Activation

JASPAR motifs

Motif	Name	Family
MA2678.1	IRX1	TALE-type HD

JASPAR matrix evidence (PMIDs): PMID:16203991

Upstream regulators (CollecTRI, top): IRX1

miRNA regulators (miRDB)

53 targeting IRX1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-579-3P	99.86	71.66	3628

Literature-anchored findings (GeneRIF, showing 20)

• Frequent methylation of IRX1 gene is associated with head and neck squamous cell carcinoma (PMID:18559491)
• Results verify IRX1, EBF3, SLC5A8, SEPT9, and FUSSEL18 as valid methylation markers in two separate sets of HNSCC specimens; also preliminarily show a trend between HPV16 positivity and target gene hypermethylation of IRX1, EBF3, SLC5A8, and SEPT9. (PMID:20029986)
• Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma. (PMID:20440264)
• IRX1 could potentially serve as a biomarker for gastric cancer. (PMID:20440264)
• enforcing IRX1 expression effectively suppresses peritoneal spreading and pulmonary metastasis via anti-angiogenesis and anti-VM mechanisms, in addition to previously found cell growth and invasion. (PMID:21602894)
• Helicobacter pylori infection contributes to IRX1 promoter methylation in gastric mucosa. (PMID:21649733)
• Findings suggest that methylation-associated down-regulation of EBF3 and IRX1 genes may play an important role in a pathogenic effect of TGF-beta on RASFs. (PMID:23456299)
• In osteosarcoma cells and lines, IRX1 overexpression was associated with hypomethylation of its own promoter. Experimental modulation in cell lines altered migration, invasion, and resistance to anoikis in vitro, and influenced lung metastasis in mice. (PMID:25822025)
• this is the first genome-wide association study of Rheumatoid Factor positivity in Rheumatoid Arthritis. Variation at the IRX1 locus on chromosome 5p15.3 is associated with the presence of Rheumatoid Factor. Our findings indicate that IRX1 and HLA-DRB1 are the strongest genetic factors for Rheumatoid Factor production in Rheumatoid Arthritis. (PMID:26815016)
• A total of three nonsynonymous mutations (p.Gln240Glu, p.Ser298Asn and p.Ala381Glu) of the IRX1 gene were verified in 215 nonsyndromic congenital heart disease patients. (PMID:28358424)
• Through a combination of sequencing studies on eighteen North Carolina macular dystrophy families, two novel overlapping duplications at the MCDR3 locus, in a gene desert downstream of IRX1 and upstream of ADAMTS16, have been reported. (PMID:28790370)
• Multiple evidences suggested that PRMT5 repressed transcription of tumor suppressor IRX1 via recruitment of DNMT3A on promoter. (PMID:29802960)
• The variant rs12517904 of the IRX1 gene is functionally associated with the development of adolescent idiopathic scoliosis in the Chinese population. For rs12517904, patients were found to have a significantly higher frequency of allele T than the controls. For rs117273909, neither the genotype nor the allele frequency was significantly different between the patients and controls. (PMID:30862593)
• IRX1 hypermethylation promotes heart failure by inhibiting CXCL14 expression. (PMID:31640472)
• Downregulated microRNA-150 upregulates IRX1 to depress proliferation, migration, and invasion, but boost apoptosis of gastric cancer cells. (PMID:31846199)
• Prognostic value of Iroquois homeobox 1 methylation in non-small cell lung cancers. (PMID:32200543)
• HOXA9/IRX1 expression pattern defines two subgroups of infant MLL-AF4-driven acute lymphoblastic leukemia. (PMID:33069783)
• The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia. (PMID:35328612)
• IRX1 is a novel gene, overexpressed in high-grade IDH-mutant astrocytomas. (PMID:37116364)
• ADRA2A and IRX1 are putative risk genes for Raynaud’s phenomenon. (PMID:37828025)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	irx1a	ENSDARG00000101831
mus_musculus	Irx1	ENSMUSG00000060969
rattus_norvegicus	Irx1	ENSRNOG00000033609

Paralogs (6): IRX4 (ENSG00000113430), MKX (ENSG00000150051), IRX6 (ENSG00000159387), IRX2 (ENSG00000170561), IRX5 (ENSG00000176842), IRX3 (ENSG00000177508)

Protein

Protein identifiers

Iroquois-class homeodomain protein IRX-1 — P78414 (reviewed: P78414)

Alternative names: Homeodomain protein IRXA1, Iroquois homeobox protein 1

All UniProt accessions (1): P78414

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Similarity. Belongs to the TALE/IRO homeobox family.

RefSeq proteins (1): NP_077313* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR003893	Iroquois_homeo	Domain
IPR008422	KN_HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site

Pfam: PF05920

UniProt features (12 total): compositionally biased region 5, region of interest 3, chain 1, DNA-binding region 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P78414-F1	55.88	0.11

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 241

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-9831926	Nephron development
R-HSA-1266738	Developmental Biology
R-HSA-9830369	Kidney development

MSigDB gene sets: 102 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_EPITHELIUM_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_METANEPHROS_DEVELOPMENT, GOBP_LOOP_OF_HENLE_DEVELOPMENT, GOBP_NEUROGENESIS, GOBP_KIDNEY_EPITHELIUM_DEVELOPMENT, GOBP_MORPHOGENESIS_OF_EMBRYONIC_EPITHELIUM, GOBP_PROXIMAL_DISTAL_PATTERN_FORMATION, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_NEPHRON_EPITHELIUM_DEVELOPMENT, GOBP_RENAL_TUBULE_DEVELOPMENT, GROSS_HYPOXIA_VIA_HIF1A_DN, GOBP_SEGMENTATION, GOBP_METANEPHRIC_NEPHRON_DEVELOPMENT

GO Biological Process (9): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of gene expression (GO:0010628), neuron differentiation (GO:0030182), cell development (GO:0048468), specification of loop of Henle identity (GO:0072086), proximal/distal pattern formation involved in metanephric nephron development (GO:0072272), metanephros development (GO:0001656), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), sequence-specific DNA binding (GO:0043565), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Kidney development	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
regulation of gene expression	2
cell differentiation	2
negative regulation of DNA-templated transcription	1
regulation of DNA-templated transcription	1
gene expression	1
positive regulation of macromolecule biosynthetic process	1
generation of neurons	1
anatomical structure development	1
cellular developmental process	1
loop of Henle development	1
specification of nephron tubule identity	1
proximal/distal pattern formation involved in nephron development	1
metanephric nephron development	1
pattern specification involved in metanephros development	1
kidney development	1
DNA-templated transcription	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
DNA binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1584 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IRX1	KCND2	Q9NZV8	839
IRX1	SMYD1	Q8NB12	786
IRX1	HAND2	P61296	698
IRX1	AKAP11	Q9UKA4	664
IRX1	KCNE4	Q8WWG9	663
IRX1	FTO	Q9C0B1	660
IRX1	ARID5B	Q14865	610
IRX1	GPD1L	Q8N335	606
IRX1	KCNE3	Q9Y6H6	594
IRX1	CACNB2	Q08289	585
IRX1	NKX2-5	P52952	567
IRX1	SCN5A	Q14524	565
IRX1	RPGRIP1L	Q68CZ1	551
IRX1	SCN1B	Q07699	546
IRX1	SCN3B	Q9NY72	536

IntAct

2 interactions, top by confidence:

A	B	Type	Score
IRX1	TRPC4AP	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (3): IRX1 (Synthetic Growth Defect), TRPC4AP (Affinity Capture-MS), IRX1 (Affinity Capture-RNA)

ESM2 similar proteins: A2A9A2, A6QQ94, A6YP92, A7MB54, B5RHS5, E9PZZ1, M0R6D8, O02786, O08934, O09029, O35085, P13297, P28360, P46153, P50548, P78413, P78414, P78415, P81067, P81068, P84550, P97830, Q12952, Q13207, Q14549, Q14774, Q2VL76, Q2VL77, Q2VL78, Q2VL79, Q2VL80, Q2VL82, Q2VL83, Q2VL84, Q2VL85, Q2VL86, Q2VL87, Q2VL88, Q2VWA4, Q5SQQ9

Diamond homologs: A1YGI6, A6NDR6, A8K0S8, A8WL06, B7ZRT8, O00470, O04136, O14770, O22300, O42261, O46339, O65685, O70477, P41779, P41817, P46606, P48000, P48001, P48002, P48731, P53147, P54269, P55347, P56659, P56660, P56664, P56665, P56669, P70284, P78412, P78413, P78414, P78415, P79937, P81067, P81068, P97367, P97368, Q0E3C3, Q0J6N4

SIGNOR signaling

19 interactions.

A	Effect	B	Mechanism
IRX1	“down-regulates quantity by repression”	BDKRB2	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	BPI	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	COL9A3	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	FGF7	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	NPTX1	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	PTGER1	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	CELF2	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	DKK3	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	PHYHIPL	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	H2BC21	“transcriptional regulation”
IRX1	“down-regulates quantity by repression”	EGR1	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	PTGS2	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	ANPEP	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	KDR	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	UGT8	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	INHBA	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	ERMAP	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	RALGPS1	“transcriptional regulation”
IRX1	“up-regulates quantity by expression”	SPON1	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

102 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	81
Likely benign	8
Benign	6

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
57222	GRCh38/hg38 5p15.33-15.32(chr5:3502990-4580491)x3	Pathogenic
57400	GRCh38/hg38 5p15.33(chr5:49978-4014647)x1	Pathogenic

SpliceAI

477 predictions. Top by Δscore:

Variant	Effect	Δscore
5:3596377:AGATG:A	donor_gain	1.0000
5:3596378:GATG:G	donor_gain	1.0000
5:3596378:GATGG:G	donor_gain	1.0000
5:3596379:ATG:A	donor_gain	1.0000
5:3596380:TG:T	donor_gain	1.0000
5:3596381:GG:G	donor_gain	1.0000
5:3596382:G:GG	donor_gain	1.0000
5:3599180:A:AG	acceptor_gain	1.0000
5:3600607:A:AG	acceptor_gain	1.0000
5:3600608:G:GG	acceptor_gain	1.0000
5:3599181:C:G	acceptor_gain	0.9900
5:3599200:C:A	acceptor_gain	0.9900
5:3599203:T:A	acceptor_gain	0.9900
5:3599204:G:A	acceptor_gain	0.9900
5:3599216:T:TA	acceptor_gain	0.9900
5:3599217:G:A	acceptor_gain	0.9900
5:3599220:TTCA:T	acceptor_loss	0.9900
5:3599222:CAGG:C	acceptor_loss	0.9900
5:3599223:A:AG	acceptor_gain	0.9900
5:3599223:AGG:A	acceptor_gain	0.9900
5:3599224:G:GG	acceptor_gain	0.9900
5:3599224:G:GT	acceptor_loss	0.9900
5:3599224:GGG:G	acceptor_gain	0.9900
5:3600603:TCGCA:T	acceptor_loss	0.9900
5:3600604:CGCA:C	acceptor_loss	0.9900
5:3600605:GCA:G	acceptor_loss	0.9900
5:3600606:CAGA:C	acceptor_loss	0.9900
5:3600606:CAGAG:C	acceptor_gain	0.9900
5:3600607:AG:A	acceptor_loss	0.9900
5:3600607:AGAGA:A	acceptor_gain	0.9900

AlphaMissense

3087 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:3599372:C:T	L142F	1.000
5:3599373:T:A	L142H	1.000
5:3599373:T:C	L142P	1.000
5:3599373:T:G	L142R	1.000
5:3599375:A:G	K143E	1.000
5:3599377:G:C	K143N	1.000
5:3599377:G:T	K143N	1.000
5:3599378:G:C	A144P	1.000
5:3599381:T:A	W145R	1.000
5:3599381:T:C	W145R	1.000
5:3599381:T:G	W145G	1.000
5:3599382:G:C	W145S	1.000
5:3599382:G:T	W145L	1.000
5:3599383:G:C	W145C	1.000
5:3599383:G:T	W145C	1.000
5:3599384:C:T	L146F	1.000
5:3599385:T:A	L146H	1.000
5:3599385:T:C	L146P	1.000
5:3599393:C:G	H149D	1.000
5:3599394:A:C	H149P	1.000
5:3599394:A:T	H149L	1.000
5:3599395:C:A	H149Q	1.000
5:3599395:C:G	H149Q	1.000
5:3599404:T:A	N152K	1.000
5:3599404:T:G	N152K	1.000
5:3599405:C:A	P153T	1.000
5:3599405:C:T	P153S	1.000
5:3599406:C:A	P153H	1.000
5:3599406:C:G	P153R	1.000
5:3599406:C:T	P153L	1.000

dbSNP variants (sampled 300 via entrez): RS1000111213 (5:3595256 C>A,G), RS1000717552 (5:3599935 G>A,T), RS1000881736 (5:3597688 A>G), RS1001331930 (5:3597452 C>T), RS1002037820 (5:3594475 C>A), RS1002090225 (5:3594289 T>A,C), RS1002096840 (5:3595770 A>G,T), RS1002499602 (5:3596175 C>A,G), RS1002714916 (5:3597408 G>A), RS1002762668 (5:3597208 G>C,T), RS1003161666 (5:3598376 G>A), RS1003545828 (5:3596832 C>G), RS1003770979 (5:3595351 G>A,C), RS1003877442 (5:3600489 G>A), RS1004389960 (5:3595069 T>C)

Disease associations

OMIM: gene MIM:606197 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

24 associations (top):

Study	Trait	p-value
GCST001491_8	Immune response to smallpox vaccine (IL-6)	9.000000e-07
GCST003330_1	Rheumatoid factor seropositivity in rheumatoid arthritis	1.000000e-08
GCST003744_3	Chronic periodontitis (mean interproximal clinical attachment level)	2.000000e-07
GCST004573_5	Iron status biomarkers (ferritin levels)	9.000000e-08
GCST005171_40	QT interval	9.000000e-08
GCST005984_15	Glomerular filtration rate	3.000000e-08
GCST006144_1	Heparin-induced thrombocytopenia	3.000000e-08
GCST006144_3	Heparin-induced thrombocytopenia	5.000000e-06
GCST006218_90	Erosive tooth wear (severe vs non-severe)	8.000000e-07
GCST006226_15	Erosive tooth wear (severe vs none or mild)	5.000000e-06
GCST006630_65	Diastolic blood pressure	5.000000e-16
GCST006903_12	Hip shape (DXA scan)	6.000000e-09
GCST007002_3	Cerebrospinal fluid t-tau levels in normal cognition	9.000000e-07
GCST007639_1	Femoral neck length	2.000000e-08
GCST007876_85	Estimated glomerular filtration rate	8.000000e-09
GCST009723_81	Vertical cup-disc ratio (adjusted for vertical disc diameter)	2.000000e-07
GCST009724_40	Vertical cup-disc ratio (multi-trait analysis)	7.000000e-10
GCST010866_105	Coronary artery disease	8.000000e-07
GCST010867_60	Coronary artery disease	6.000000e-09
GCST010988_87	Adult body size	2.000000e-10
GCST90020025_625	Waist-to-hip ratio adjusted for BMI	4.000000e-12
GCST90020026_323	Hip index	5.000000e-10
GCST90020027_1954	Waist-hip index	4.000000e-12
GCST90020028_1028	Hip circumference adjusted for BMI	4.000000e-08

EFO canonical traits (13, from GWAS)

EFO ID	Trait name
EFO:0004645	response to vaccine
EFO:0005767	rheumatoid factor measurement
EFO:0007791	rheumatoid factor seropositivity measurement
EFO:0007780	periodontal measurement
EFO:0004459	ferritin measurement
EFO:0004682	QT interval
EFO:0006336	diastolic blood pressure
EFO:0004685	hip geometry
EFO:0004760	t-tau measurement
EFO:0004511	femoral neck bone geometry
EFO:0006939	cup-to-disc ratio measurement
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects expression, decreases expression	5
methylmercuric chloride	increases expression, affects cotreatment	3
trichostatin A	increases expression, affects cotreatment	3
sodium arsenite	decreases expression	2
entinostat	decreases expression, increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	increases expression	2
bisphenol A	decreases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
arsenite	increases methylation	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment, increases expression	1
dorsomorphin	increases expression, decreases expression, affects cotreatment	1
Resveratrol	affects cotreatment, decreases expression	1
Decitabine	affects expression, affects methylation	1
Atrazine	increases expression	1
Vehicle Emissions	decreases methylation	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Mitoxantrone	affects response to substance	1
Nickel	decreases expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Smoke	increases expression	1
Tretinoin	decreases expression	1
Triclosan	increases expression	1
1-Methyl-4-phenylpyridinium	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1
Copper Sulfate	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A3H7	SEES3-1V human IRX1, clone1	Embryonic stem cell	Male
CVCL_A3H8	SEES3-1V human IRX1, clone2	Embryonic stem cell	Male
CVCL_A3H9	SEES3-1V human IRX1, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.