FOXN3

Summary

FOXN3 (forkhead box N3, HGNC:1928) is a protein-coding gene on chromosome 14q31.3-q32.11, encoding Forkhead box protein N3 (O00409). Acts as a transcriptional repressor.

This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms.

Source: NCBI Gene 1112 — RefSeq curated summary.

At a glance

• GWAS associations: 25
• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_005197

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1928
Approved symbol	FOXN3
Name	forkhead box N3
Location	14q31.3-q32.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000053254
Ensembl biotype	protein_coding
OMIM	602628
Entrez	1112

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 25 protein_coding, 5 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000261302, ENST00000345097, ENST00000553353, ENST00000553840, ENST00000553904, ENST00000554005, ENST00000555010, ENST00000555034, ENST00000555353, ENST00000555658, ENST00000555855, ENST00000556541, ENST00000556916, ENST00000557258, ENST00000557261, ENST00000557496, ENST00000557572, ENST00000557718, ENST00000615335, ENST00000884418, ENST00000884419, ENST00000884420, ENST00000884421, ENST00000884422, ENST00000884423, ENST00000884424, ENST00000922268, ENST00000950235, ENST00000950236, ENST00000950237, ENST00000950238, ENST00000950239

RefSeq mRNA: 2 — MANE Select: NM_005197 NM_001085471, NM_005197

CCDS: CCDS32138, CCDS41977

Canonical transcript exons

ENST00000557258 — 6 exons

Exon	Start	End
ENSE00000659606	89180701	89180806
ENSE00001217927	89416871	89417233
ENSE00001385423	89411934	89412490
ENSE00002478301	89156177	89162969
ENSE00003630447	89280950	89281014
ENSE00003667905	89350672	89350808

Expression profiles

Bgee: expression breadth ubiquitous, 300 present calls, max score 98.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.9272 / max 495.0200, expressed in 1754 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
144445	11.9996	1552
144436	7.3469	1597
144435	2.7782	1162
144425	1.9904	843
144446	0.8058	191
144434	0.5606	289
144433	0.3910	202
144441	0.0548	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
paraflocculus	UBERON:0005351	98.72	gold quality
tendon of biceps brachii	UBERON:0008188	98.35	gold quality
nipple	UBERON:0002030	98.18	gold quality
saphenous vein	UBERON:0007318	98.07	gold quality
skin of hip	UBERON:0001554	97.63	gold quality
upper arm skin	UBERON:0004263	97.57	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.48	gold quality
upper leg skin	UBERON:0004262	97.46	gold quality
synovial joint	UBERON:0002217	97.28	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	97.08	gold quality
cardia of stomach	UBERON:0001162	96.79	gold quality
vastus lateralis	UBERON:0001379	96.69	gold quality
lower lobe of lung	UBERON:0008949	96.68	gold quality
quadriceps femoris	UBERON:0001377	96.57	gold quality
gluteal muscle	UBERON:0002000	96.57	gold quality
superficial temporal artery	UBERON:0001614	96.53	gold quality
tendon	UBERON:0000043	96.50	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.50	gold quality
colonic epithelium	UBERON:0000397	96.41	gold quality
blood vessel layer	UBERON:0004797	96.41	gold quality
jejunum	UBERON:0002115	96.37	gold quality
urethra	UBERON:0000057	96.36	gold quality
body of tongue	UBERON:0011876	96.32	gold quality
biceps brachii	UBERON:0001507	96.29	gold quality
cerebellar vermis	UBERON:0004720	96.29	gold quality
deltoid	UBERON:0001476	96.23	gold quality
epithelium of nasopharynx	UBERON:0001951	96.08	gold quality
nasopharynx	UBERON:0001728	96.06	gold quality
superior surface of tongue	UBERON:0007371	96.03	gold quality
penis	UBERON:0000989	96.02	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	38.79
E-CURD-119	yes	20.22
E-HCAD-25	yes	16.48
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
PIM2	Repression

JASPAR motifs

Motif	Name	Family
MA1489.1	FOXN3	FOX

JASPAR matrix evidence (PMIDs): PMID:30826165

miRNA regulators (miRDB)

197 targeting FOXN3, 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-6867-5P	100.00	82.21	3464
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-4482-3P	99.98	72.50	3147

Literature-anchored findings (GeneRIF, showing 24)

• Data suggest that CHES1 recruits Ski-interacting protein (SKIP) to repress genes important for tumorigenesis and the response to cancer treatments. (PMID:16102918)
• Meninis involved in the activation of S-phase arrest in multple endocrein neoplasia by interacting with CHES1. (PMID:16951149)
• Two novel homozygously deleted genes in hepatocellular carcinomas are caspase 3 and CHES1. (PMID:17983802)
• FOXN3 might contribute to the observed phenotype. (PMID:18074379)
• Four genes previously not examined in that respect in laryngeal carcinoma, occurred to be good markers of the neoplasm. They are: metal-proteinase ADAM12, cyclin-dependent kinase 2-CDK2, kinesin 14-KIF14, suppressor 1 of checkpoint-CHES1. (PMID:19609547)
• the Foxn3 mutation leads to partial embryonic and postnatal lethality, growth retardation, eye formation defects, dental anomalies and craniofacial defects. (PMID:20691664)
• MicroRNA-574-5p has a critical role in TLR9 signaling enhanced tumor progression via down-regulating checkpoint suppressor 1 (PMID:23133627)
• CHES1 decreases protein synthesis and cell proliferation in tumor cell lines but not in normal fibroblasts. (PMID:24403608)
• MEN1 patients with MEN1 mutations leading to CHES1-loss of interaction have a higher risk of malignant pancreatic neuroendocrine tumors with an aggressive course of disease and disease-related death. (PMID:25210877)
• Foxn3 is a direct transcriptional suppressor of N-cadherin in colorectal metastasis. (PMID:26069251)
• FOXN3 functions as a tumor suppressor in hepatocellular carcinoma by downregulating the expression of E2F5. (PMID:27259277)
• the rs8004664 risk allele drives excessive expression of FOXN3 during fasting and that FOXN3 regulates fasting blood glucose. (PMID:27292639)
• the FOXN3-NEAT1-SIN3A complex promotes epithelial-to-mesenchymal transition and invasion of breast cancer cells in vitro as well as dissemination and metastasis of breast cancer in vivo (PMID:28805661)
• these results identified a negative cross-regulatory loop between ERalpha and CHES1 that was required for growth of breast cancer cells, it might uncover novel insight into molecular mechanism of CHES1 involved in breast cancer and provide new avenues for molecular-targeted therapy in hormone-regulated breast cancer. (PMID:29752474)
• liver FOXN3 and glucagon control fasting glucose. (PMID:29996093)
• FOXN3 was notably downregulated in osteosarcoma (OS) tissues and the expression of FOXN3 was negatively correlated with tumor size, metastasis and TNM stage. Also, FOXN3 suppressed the proliferation, migration and invasion of osteosarcoma cells. Furthermore, FOXN3 was demonstrated to transcriptionally suppress SIRT6 expression, thereby inhibiting MMP9 secretion. (PMID:30483801)
• We present co-crystal structures of the FoxN3 DNA binding domain bound to the FKH and FHL sites, respectively. FoxN3 adopts a similar conformation to recognize both motifs, making contacts with different DNA bases using the same amino acids. However, the DNA structure is different in the two complexes (PMID:30826165)
• The clinical and prognostic significance of FOXN3 downregulation in acute myeloid leukaemia. (PMID:32078244)
• MicroRNA-574-5p directly targets FOXN3 to mediate thyroid cancer progression via Wnt/beta-catenin signaling pathway. (PMID:32284251)
• FOXN3 suppresses the growth and invasion of papillary thyroid cancer through the inactivation of Wnt/beta-catenin pathway. (PMID:32619584)
• miR-574-5p Targets FOXN3 to Regulate the Invasion of Nasopharyngeal Carcinoma Cells via Wnt/beta-Catenin Pathway. (PMID:33317407)
• FOXN3 inhibits cell proliferation and invasion via modulating the AKT/MDM2/p53 axis in human glioma. (PMID:34511432)
• FOXN3 inhibits the progression of ovarian cancer through negatively regulating the expression of RPS15A. (PMID:37016167)
• CHES1 modulated tumorigenesis and senescence of pancreas cancer cells through repressing AKR1B10. (PMID:38718846)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ches1	ENSDARG00000043553
mus_musculus	Foxn3	ENSMUSG00000033713
rattus_norvegicus	Foxn3	ENSRNOG00000004709

Paralogs (2): FOXN4 (ENSG00000139445), FOXN2 (ENSG00000170802)

Protein

Protein identifiers

Forkhead box protein N3 — O00409 (reviewed: O00409)

Alternative names: Checkpoint suppressor 1

All UniProt accessions (10): O00409, G3V3A7, G3V4N5, G3V5C7, H0YJ22, H0YJ43, H0YJ54, H0YJ94, H0YJG3, H0YJY0

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints).

Subunit / interactions. Interacts through its C-terminus with the C-terminus of SNW1/SKIP.

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
O00409-1	1	yes
O00409-2	2

RefSeq proteins (2): NP_001078940, NP_005188* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001766	Fork_head_dom	Domain
IPR018122	TF_fork_head_CS_1	Conserved_site
IPR030456	TF_fork_head_CS_2	Conserved_site
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily
IPR047119	FOXN2/3-like	Family
IPR047404	FH_FOXN3	Domain

Pfam: PF00250

UniProt features (24 total): helix 5, modified residue 4, compositionally biased region 4, strand 3, region of interest 3, chain 1, DNA-binding region 1, splice variant 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
6NCE	X-RAY DIFFRACTION	2.6
6NCM	X-RAY DIFFRACTION	2.7

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O00409-F1	58.28	0.17

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 (4): 85, 97, 448, 83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 425 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_UP, RRAGTTGT_UNKNOWN, YAATNRNNNYNATT_UNKNOWN, TAATAAT_MIR126, CCAWYNNGAAR_UNKNOWN, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GAANYNYGACNY_UNKNOWN, NKX25_02, PEREZ_TP63_TARGETS, TTTGTAG_MIR520D, SP3_Q3, ATACCTC_MIR202, AAGCCAT_MIR135A_MIR135B, GOBP_CELL_CYCLE_PHASE_TRANSITION

GO Biological Process (5): regulation of DNA-templated transcription (GO:0006355), mitotic G2 DNA damage checkpoint signaling (GO:0007095), negative regulation of DNA-templated transcription (GO:0045892), craniofacial suture morphogenesis (GO:0097094), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (6): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), cis-regulatory region sequence-specific DNA binding (GO:0000987), DNA-binding transcription factor activity (GO:0003700), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	3
DNA-templated transcription	2
transcription cis-regulatory region binding	2
regulation of gene expression	1
regulation of RNA biosynthetic process	1
mitotic G2 phase	1
mitotic DNA damage checkpoint signaling	1
mitotic G2/M transition checkpoint	1
negative regulation of RNA biosynthetic process	1
anatomical structure morphogenesis	1
bone morphogenesis	1
cranial skeletal system development	1
transcription by RNA polymerase II	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transcription regulator activity	1
nucleic acid binding	1
binding	1
DNA binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1209 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FOXN3	SIN3A	Q96ST3	953
FOXN3	MEN1	O00255	819
FOXN3	SNW1	Q13573	814
FOXN3	ATR	Q13535	676
FOXN3	CYP24A1	Q07973	586
FOXN3	PABPN1	Q86U42	576
FOXN3	HDAC3	O15379	566
FOXN3	HDAC1	Q13547	543
FOXN3	HDAC2	Q92769	538
FOXN3	HDAC8	Q9BY41	508
FOXN3	CYP27B1	O15528	502
FOXN3	NCOA1	Q15788	475
FOXN3	TTC16	Q8NEE8	458
FOXN3	HOXD13	P35453	438
FOXN3	MYOG	P15173	431

IntAct

17 interactions, top by confidence:

A	B	Type	Score
FOXN3	RFX1	psi-mi:“MI:0914”(association)	0.530
SNW1	FOXN3	psi-mi:“MI:0915”(physical association)	0.510
FOXN3	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
SRPK2	FOXN3	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
FOXN3	FOXR2	psi-mi:“MI:0915”(physical association)	0.400
PCNA	FOXN3	psi-mi:“MI:0915”(physical association)	0.370
FOXN3	FOXN3	psi-mi:“MI:0914”(association)	0.350
CCNO	FOXN3	psi-mi:“MI:0914”(association)	0.350
FOXN3	IGLL5	psi-mi:“MI:0914”(association)	0.350
FOXN3	RFPL4A	psi-mi:“MI:0914”(association)	0.350
TOR1AIP2	FOXN3	psi-mi:“MI:0914”(association)	0.350
EXOSC8	FOXN3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (65): CHSY3 (Affinity Capture-MS), CHSY1 (Affinity Capture-MS), FOXO3B (Affinity Capture-MS), HRNR (Affinity Capture-MS), KBTBD7 (Affinity Capture-MS), FOXN3 (Affinity Capture-MS), RFX2 (Affinity Capture-MS), RFX3 (Affinity Capture-MS), RFX1 (Affinity Capture-MS), ZBTB34 (Affinity Capture-MS), BTRC (Affinity Capture-MS), FBXW11 (Affinity Capture-MS), DDB2 (Affinity Capture-MS), FOXN3 (Affinity Capture-RNA), FOXN3 (Reconstituted Complex)

ESM2 similar proteins: A0JPB4, A1L1J6, A2VDW9, A4IFJ6, O00409, O08876, O08900, O13089, O15060, O15062, O42410, O57415, O60315, O75626, O89091, P14404, P25932, P36197, P37275, P55878, P55879, P81183, Q03267, Q0VDT2, Q13422, Q33BP8, Q3BJS3, Q3UH06, Q499D0, Q5R9W9, Q5T0B9, Q5ZLR2, Q5ZM39, Q60636, Q62255, Q62947, Q64318, Q6DBW0, Q6NRM0, Q6XDT4

Diamond homologs: A0A8V0YY16, A1L1S5, A2BGM5, A8MTJ6, B5RHS5, D3Z120, O00358, O00409, O15353, O54743, O60129, O70220, O88470, O93529, P32027, P32028, P32030, P32314, P42128, P55316, P56260, P58012, Q00939, Q12946, Q12947, Q12948, Q12951, Q13461, Q1A1A1, Q1A1A2, Q1A1A3, Q1A1A4, Q1A1A5, Q1A1A6, Q28BS5, Q28D67, Q28F43, Q28G71, Q28H65, Q28HT3

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
FOXN3	“down-regulates quantity by repression”	PIM2	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3129 predictions. Top by Δscore:

Variant	Effect	Δscore
14:89162967:TTC:T	acceptor_gain	1.0000
14:89180696:CTTA:C	donor_loss	1.0000
14:89180697:TTACC:T	donor_loss	1.0000
14:89180698:TA:T	donor_loss	1.0000
14:89180699:A:AC	donor_gain	1.0000
14:89180699:A:AT	donor_loss	1.0000
14:89180700:C:CC	donor_gain	1.0000
14:89180700:CCT:C	donor_gain	1.0000
14:89180807:C:CC	acceptor_gain	1.0000
14:89280945:CCTA:C	donor_loss	1.0000
14:89280946:CTA:C	donor_loss	1.0000
14:89280947:TA:T	donor_loss	1.0000
14:89280948:A:AT	donor_loss	1.0000
14:89280949:C:CG	donor_loss	1.0000
14:89281010:ATGTG:A	acceptor_gain	1.0000
14:89281011:TGTG:T	acceptor_gain	1.0000
14:89281012:GTG:G	acceptor_gain	1.0000
14:89281013:TG:T	acceptor_gain	1.0000
14:89281015:C:CC	acceptor_gain	1.0000
14:89162965:CATTC:C	acceptor_gain	0.9900
14:89162966:ATTC:A	acceptor_gain	0.9900
14:89162968:TC:T	acceptor_gain	0.9900
14:89162969:CC:C	acceptor_gain	0.9900
14:89162969:CCT:C	acceptor_loss	0.9900
14:89162970:C:CC	acceptor_gain	0.9900
14:89162978:C:CT	acceptor_gain	0.9900
14:89162979:G:T	acceptor_gain	0.9900
14:89162984:C:CT	acceptor_gain	0.9900
14:89162985:A:T	acceptor_gain	0.9900
14:89162986:G:C	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000006538 (14:89526245 T>C), RS1000008413 (14:89241565 C>T), RS1000009008 (14:89234487 G>A,C), RS1000009946 (14:89385888 G>A), RS1000013753 (14:89567204 T>G), RS1000020203 (14:89553346 T>A), RS1000036917 (14:89356591 T>C), RS1000039018 (14:89248685 G>A), RS1000057938 (14:89235359 G>C), RS1000059300 (14:89601197 G>T), RS1000060974 (14:89391746 T>C), RS1000066784 (14:89254933 A>T), RS1000067419 (14:89202266 C>G), RS1000067993 (14:89472463 G>A), RS1000087569 (14:89609789 A>G)

Disease associations

OMIM: gene MIM:602628 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

25 associations (top):

Study	Trait	p-value
GCST001527_13	Fasting blood glucose (BMI interaction)	3.000000e-06
GCST001991_2	Weight loss (gastric bypass surgery)	5.000000e-06
GCST002938_34	Copper levels	7.000000e-06
GCST003134_11	Cerebrospinal fluid clusterin levels	5.000000e-06
GCST003657_5	Attention deficit hyperactivity disorder symptom score	3.000000e-06
GCST003783_11	Multiple system atrophy (pathologically confirmed)	1.000000e-07
GCST004746_43	Small cell lung carcinoma	6.000000e-06
GCST005186_14	Fasting blood glucose	1.000000e-06
GCST005316_535	Intelligence (MTAG)	1.000000e-11
GCST005316_536	Intelligence (MTAG)	3.000000e-09
GCST005688_12	Idiopathic intracranial hypertension	1.000000e-06
GCST006269_735	General cognitive ability	1.000000e-08
GCST006622_23	Neonatal cytokine/chemokine levels (fetal genetic effect)	9.000000e-07
GCST006626_30	Pulse pressure	3.000000e-11
GCST006979_1011	Heel bone mineral density	7.000000e-11
GCST007325_11	General risk tolerance (MTAG)	8.000000e-09
GCST008158_94	Body mass index	4.000000e-06
GCST008469_12	Liver fibrosis in non-alcoholic fatty liver disease	9.000000e-06
GCST008810_46	Smoking initiation (ever regular vs never regular)	3.000000e-08
GCST009186_10	Insular cortex volume	3.000000e-06
GCST009391_699	Metabolite levels	8.000000e-06
GCST010242_70	HDL cholesterol levels	5.000000e-09
GCST010796_3880	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-10
GCST010796_3881	Electrocardiogram morphology (amplitude at temporal datapoints)	1.000000e-08
GCST010796_3882	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-09

EFO canonical traits (14, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0005245	body weight loss
EFO:0007860	ADHD symptom measurement
EFO:0004337	intelligence
EFO:0004747	protein measurement
EFO:0007959	fetal genotype effect measurement
EFO:0008191	obsolete_interleukin 8 measurement
EFO:0005763	pulse pressure measurement
EFO:0009270	heel bone mineral density
EFO:0008579	risk-taking behaviour
EFO:0005670	smoking initiation
EFO:0007745	lactate measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	6
bisphenol A	increases expression, decreases expression, decreases methylation	3
Air Pollutants	decreases expression, increases abundance	3
Tobacco Smoke Pollution	decreases expression, increases methylation	3
sodium arsenite	increases abundance, increases expression, affects methylation	2
Arsenic	increases expression, affects methylation, increases abundance	2
Tetrachlorodibenzodioxin	decreases expression	2
Valproic Acid	decreases expression, decreases methylation	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Aflatoxin B1	decreases methylation, affects methylation	2
Particulate Matter	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
1-cyclopropyl-4-(4-((5-methyl-3-(3-(4-(trifluoromethoxy)phenyl)-1,2,4-oxadiazol-5-yl)-1H-pyrazol-1-yl)methyl)pyridin-2-yl)piperazine	decreases reaction, increases expression	1
GSK-J4	increases expression	1
triphenyl phosphate	affects expression	1
potassium perchlorate	decreases expression	1
beta-lapachone	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	affects methylation	1
coumarin	decreases phosphorylation	1
cupric oxide	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	increases expression	1
abrine	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases expression, increases response to substance	1
Resveratrol	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Leflunomide	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_A2C4	SEES3-1V human FOXN3, clone1	Embryonic stem cell	Male
CVCL_A2C5	SEES3-1V human FOXN3, clone2	Embryonic stem cell	Male
CVCL_A2C6	SEES3-1V human FOXN3, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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