HOXC9

Summary

HOXC9 (homeobox C9, HGNC:5130) is a protein-coding gene on chromosome 12q13.13, encoding Homeobox protein Hox-C9 (P31274). Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12.

Source: NCBI Gene 3225 — RefSeq curated summary.

At a glance

• GWAS associations: 16
• Clinical variants (ClinVar): 34 total
• MANE Select transcript: NM_006897

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:5130
Approved symbol	HOXC9
Name	homeobox C9
Location	12q13.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000180806
Ensembl biotype	protein_coding
OMIM	142971
Entrez	3225

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000303450, ENST00000504557, ENST00000508190

RefSeq mRNA: 1 — MANE Select: NM_006897 NM_006897

CCDS: CCDS8869

Canonical transcript exons

ENST00000303450 — 2 exons

Exon	Start	End
ENSE00001151626	54002430	54003337
ENSE00001151635	54000161	54000726

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.35.

FANTOM5 (CAGE): breadth broad, TPM avg 4.9691 / max 177.2784, expressed in 866 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125845	3.1066	755
125847	0.8316	434
125846	0.4268	301
125848	0.3561	189
125844	0.2480	129

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	91.35	gold quality
gastrocnemius	UBERON:0001388	90.99	gold quality
muscle of leg	UBERON:0001383	90.66	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.59	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.06	gold quality
metanephros cortex	UBERON:0010533	84.25	gold quality
vastus lateralis	UBERON:0001379	83.68	silver quality
subcutaneous adipose tissue	UBERON:0002190	83.58	gold quality
tibialis anterior	UBERON:0001385	83.43	silver quality
popliteal artery	UBERON:0002250	81.23	gold quality
tibial artery	UBERON:0007610	81.22	gold quality
skin of leg	UBERON:0001511	80.78	gold quality
kidney epithelium	UBERON:0004819	80.74	gold quality
tibial nerve	UBERON:0001323	79.81	gold quality
skin of abdomen	UBERON:0001416	79.63	gold quality
cortex of kidney	UBERON:0001225	79.31	gold quality
zone of skin	UBERON:0000014	78.22	gold quality
left uterine tube	UBERON:0001303	78.03	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.53	gold quality
adult mammalian kidney	UBERON:0000082	77.03	gold quality
metanephros	UBERON:0000081	76.77	gold quality
tendon	UBERON:0000043	76.03	gold quality
small intestine Peyer’s patch	UBERON:0003454	75.67	gold quality
ileal mucosa	UBERON:0000331	75.57	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	75.31	silver quality
skin of hip	UBERON:0001554	75.05	gold quality
kidney	UBERON:0002113	74.99	gold quality
buccal mucosa cell	CL:0002336	74.50	silver quality
renal medulla	UBERON:0000362	73.95	gold quality
adipose tissue	UBERON:0001013	73.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.66

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

Target	Regulation
CXCL8
HOXB8	Repression
HOXC8	Unknown
STAB2

JASPAR motifs

Motif	Name	Family
MA0485.2	HOXC9	HOX
MA0485.3	HOXC9	HOX

JASPAR matrix evidence (PMIDs): PMID:9079637

Upstream regulators (CollecTRI, top): EZH2

miRNA regulators (miRDB)

61 targeting HOXC9, 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-12118	100.00	65.88	1270
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-6516-3P	99.65	68.57	1238
HSA-MIR-567	99.63	68.57	1219

Literature-anchored findings (GeneRIF, showing 16)

• Up-regulation of HOXC9 was detected in a set of 54 astrocytomas of different grades and significantly associated with malignancy. (PMID:17588684)
• Methylated state of this set of genes may be more specific to the late rather than the early stage of NSCLC. (PMID:19506903)
• The data identify HOXC9 as an endothelial cell active transcriptional repressor promoting the resting, antiangiogenic endothelial cell phenotype in an interleukin 8-dependent manner (PMID:21493894)
• HOXC9 links cell-cycle exit and neuronal differentiation and is a prognostic marker in neuroblastoma. (PMID:21507931)
• We did not find any potential pathological mutations in the Hoxc9 gene among Chinese patients with congenital heart disease. (PMID:22106857)
• HoxC9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma. (PMID:23579273)
• HOXC9 coordinates diverse cellular processes associated with differentiation by directly activating and repressing the transcription of distinct sets of genes. (PMID:24274069)
• Results provide a set of the essential genes in the miR-193a-3p/HOXC9/DNA damage response/oxidative stress pathway axis as the diagnostic targets for the guided anti-bladder cancer chemotherapy. (PMID:25444900)
• downregulation of HOXC9 releases its transcriptional inhibition of DAPK1, resulting in the activation of the DAPK1-Beclin1 pathway, which induces autophagy in glioblastoma cells (PMID:26582930)
• HOXC9 and HOXC10 may play an important role in the development of obesity, adverse fat distribution, and subsequent alterations in whole-body metabolism and adipose tissue function. (PMID:26647900)
• HOXC9 knockdown inhibited the metastasis and stem cell-like phenotype of GC cells without significant effects on cell proliferation as a direct target of miR-26a. (PMID:30205370)
• Transcription factor homeobox C9 (HOXC9) may play a critical role in colorectal cancer (CRC) progression and serve as a potential marker of poor prognosis in CRC. (PMID:31414766)
• HOXC9 overexpression is associated with gastric cancer progression and a prognostic marker for poor survival in gastric cancer patients. (PMID:32816159)
• Upregulation of HOXC9 generates interferon-gamma resistance in gastric cancer by inhibiting the DAPK1/RIG1/STAT1 axis. (PMID:34159686)
• circRNA-mediated upregulation of HOXC9 is correlated with poor outcome and immune microenvironment infiltrates in LUAD. (PMID:36272177)
• HOXC9 characterizes a suppressive tumor immune microenvironment and integration with multiple immune biomarkers predicts response to PD-1 blockade plus chemotherapy in lung adenocarcinoma. (PMID:38446596)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	hoxc9a	ENSDARG00000092809
mus_musculus	Hoxc9	ENSMUSG00000036139
rattus_norvegicus	Hoxc9	ENSRNOG00000016199

Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB5 (ENSG00000120075), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC11 (ENSG00000123388), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD3 (ENSG00000128652), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), HOXD13 (ENSG00000128714), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), TLX3 (ENSG00000164438), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

Homeobox protein Hox-C9 — P31274 (reviewed: P31274)

Alternative names: Homeobox protein Hox-3B

All UniProt accessions (1): P31274

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Subunit / interactions. Interacts with Geminin/GMNN, which inhibits transcriptional activity.

Subcellular location. Nucleus.

Similarity. Belongs to the Abd-B homeobox family.

RefSeq proteins (1): NP_008828* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR006711	Hox9_activation_N	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017112	HXA9/HXB9/HXC9	Family
IPR017970	Homeobox_CS	Conserved_site
IPR020479	HD_metazoa	Domain

Pfam: PF00046, PF04617

UniProt features (11 total): helix 3, strand 2, chain 1, DNA-binding region 1, region of interest 1, modified residue 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
2LP0	SOLUTION NMR
2MSY	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P31274-F1	65.91	0.24

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): 159

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GOBP_PROXIMAL_DISTAL_PATTERN_FORMATION, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_ANTERIOR_POSTERIOR_PATTERN_SPECIFICATION, GOBP_EMBRYONIC_ORGAN_MORPHOGENESIS, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE, ABBUD_LIF_SIGNALING_1_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, DOUGLAS_BMI1_TARGETS_UP, GOBP_EMBRYO_DEVELOPMENT

GO Biological Process (8): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), anterior/posterior pattern specification (GO:0009952), proximal/distal pattern formation (GO:0009954), negative regulation of cell cycle (GO:0045786), embryonic skeletal system morphogenesis (GO:0048704), regulation of DNA-templated transcription (GO:0006355), embryonic skeletal system development (GO:0048706)

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 factor activity (GO:0003700), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), aggresome (GO:0016235), transcription repressor complex (GO:0017053)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
regionalization	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
cellular anatomical structure	2
gene expression	1
RNA biosynthetic process	1
transcription by RNA polymerase II	1
cell cycle	1
negative regulation of cellular process	1
regulation of cell cycle	1
embryonic organ morphogenesis	1
skeletal system morphogenesis	1
embryonic skeletal system development	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
skeletal system development	1
chordate embryonic development	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
inclusion body	1
transcription regulator complex	1

Protein interactions and networks

STRING

948 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HOXC9	TMEM26	Q6ZUK4	716
HOXC9	ISL1	P20663	669
HOXC9	LHX8	Q68G74	664
HOXC9	HOXB7	P09629	552
HOXC9	MEIS1	O00470	545
HOXC9	HOXC4	P09017	544
HOXC9	UCP1	P25874	532
HOXC9	HOXB5	P09067	527
HOXC9	ZIC1	Q15915	517
HOXC9	PRDM16	Q9HAZ2	514
HOXC9	LOXL4	Q96JB6	499
HOXC9	ING5	Q8WYH8	497
HOXC9	HOXB4	P17483	491
HOXC9	CIDEA	O60543	490
HOXC9	SHOX2	O60902	487

IntAct

102 interactions, top by confidence:

A	B	Type	Score
LPXN	HOXC9	psi-mi:“MI:0915”(physical association)	0.780
HOXC9	AHCYL1	psi-mi:“MI:0914”(association)	0.640
HOXC9	GMNN	psi-mi:“MI:0407”(direct interaction)	0.620
GMNN	HOXC9	psi-mi:“MI:0407”(direct interaction)	0.620
HOXC9	PBX2	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	MAGED1	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	PAX8	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	HOXC9	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	TLE5	psi-mi:“MI:0915”(physical association)	0.560
PAX6	HOXC9	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	SPMIP9	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	MSX2	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	POU2AF1	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	UFSP1	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	KRTAP6-2	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	NFKBID	psi-mi:“MI:0915”(physical association)	0.560
HOXC9	E2	psi-mi:“MI:0915”(physical association)	0.550
E2	HOXC9	psi-mi:“MI:0915”(physical association)	0.550
PIGT	ZNF609	psi-mi:“MI:0914”(association)	0.530
ARIH1	SPOP	psi-mi:“MI:0914”(association)	0.530
IFNA10	HOXC9	psi-mi:“MI:0915”(physical association)	0.370
IFNA21	HOXC9	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (68): LPXN (Two-hybrid), IDE (Affinity Capture-MS), AHCYL2 (Affinity Capture-MS), AHCYL1 (Affinity Capture-MS), HOXC9 (Affinity Capture-MS), AHCYL2 (Affinity Capture-MS), HOXC9 (Affinity Capture-MS), HOXC9 (Affinity Capture-MS), HOXC9 (Affinity Capture-MS), IDE (Affinity Capture-MS), AHCYL1 (Affinity Capture-MS), NDUFS1 (Affinity Capture-MS), HOXC9 (Affinity Capture-MS), HOXC9 (Two-hybrid), HOXC9 (Two-hybrid)

ESM2 similar proteins: A1YGA4, A2D635, A2T6F8, A2T779, A2T7T2, A5YC49, A6NJ46, A9L937, B0VXK3, F1Q4R9, O35137, O42173, O42367, O43248, O43364, P09019, P09025, P09632, P09633, P17278, P17481, P17482, P20615, P24342, P31245, P31246, P31259, P31270, P31272, P31273, P31274, P31311, P32442, P50221, Q08727, Q0VCS4, Q1KKR7, Q1KKT2, Q1KKY2, Q1KKZ4

Diamond homologs: A1YFT7, A2D5V0, A2D635, A2T6F8, A2T7D1, A2T7H7, B5DFK3, O42502, O42503, O42506, O43248, P09013, P09014, P09023, P09025, P09067, P09079, P09087, P09631, P09632, P09633, P10179, P14838, P15861, P17481, P17482, P17509, P18863, P18866, P20615, P23459, P23813, P24340, P24341, P24342, P28356, P28357, P28358, P28359, P31257

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

493 predictions. Top by Δscore:

Variant	Effect	Δscore
12:54000727:G:GG	donor_gain	1.0000
12:54002419:T:TA	acceptor_gain	1.0000
12:54002420:G:A	acceptor_gain	1.0000
12:54002428:A:AG	acceptor_gain	1.0000
12:54002429:G:GG	acceptor_gain	1.0000
12:54002429:GGC:G	acceptor_gain	1.0000
12:54002429:GGCA:G	acceptor_gain	1.0000
12:54000187:C:CA	acceptor_gain	0.9900
12:54000722:CCCCA:C	donor_gain	0.9900
12:54000723:CCCA:C	donor_gain	0.9900
12:54000724:CCA:C	donor_gain	0.9900
12:54000725:CA:C	donor_gain	0.9900
12:54000725:CAGTA:C	donor_loss	0.9900
12:54000726:AGTA:A	donor_loss	0.9900
12:54000727:GTAA:G	donor_loss	0.9900
12:54000728:T:A	donor_loss	0.9900
12:54002424:CTCCA:C	acceptor_loss	0.9900
12:54002426:CCAG:C	acceptor_loss	0.9900
12:54002428:A:C	acceptor_loss	0.9900
12:54002428:AG:A	acceptor_gain	0.9900
12:54002428:AGGC:A	acceptor_loss	0.9900
12:54002429:G:A	acceptor_loss	0.9900
12:54002429:G:GA	acceptor_gain	0.9900
12:54002429:GG:G	acceptor_gain	0.9900
12:54002429:GGCAA:G	acceptor_gain	0.9900
12:54002710:G:T	donor_gain	0.9900
12:54000732:T:G	donor_gain	0.9800
12:54002771:A:T	donor_gain	0.9700
12:54002663:G:GT	donor_gain	0.9500
12:54002818:G:GT	donor_gain	0.9500

AlphaMissense

1701 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:54002447:T:A	W186R	1.000
12:54002447:T:C	W186R	1.000
12:54002449:G:C	W186C	1.000
12:54002449:G:T	W186C	1.000
12:54002457:C:A	A189D	1.000
12:54002469:G:C	R193T	1.000
12:54002469:G:T	R193M	1.000
12:54002470:G:C	R193S	1.000
12:54002470:G:T	R193S	1.000
12:54002471:A:G	K194E	1.000
12:54002473:G:C	K194N	1.000
12:54002473:G:T	K194N	1.000
12:54002474:A:G	K195E	1.000
12:54002476:G:C	K195N	1.000
12:54002476:G:T	K195N	1.000
12:54002477:C:A	R196S	1.000
12:54002477:C:G	R196G	1.000
12:54002477:C:T	R196C	1.000
12:54002478:G:A	R196H	1.000
12:54002484:C:A	P198H	1.000
12:54002486:T:A	Y199N	1.000
12:54002486:T:C	Y199H	1.000
12:54002486:T:G	Y199D	1.000
12:54002487:A:C	Y199S	1.000
12:54002487:A:G	Y199C	1.000
12:54002490:C:T	T200I	1.000
12:54002492:A:G	K201E	1.000
12:54002494:G:C	K201N	1.000
12:54002494:G:T	K201N	1.000
12:54002499:A:C	Q203P	1.000

dbSNP variants (sampled 300 via entrez): RS1000377526 (12:54000843 G>A), RS1000467328 (12:54002349 G>A,C), RS1001251239 (12:53999595 T>C), RS1001286191 (12:53999315 G>T), RS1001306719 (12:53999220 G>A), RS1002728112 (12:53998895 C>A,T), RS1002821716 (12:53999221 G>A), RS1002918458 (12:54000815 G>A), RS1003192865 (12:54003236 C>G), RS1003738101 (12:54003466 G>A,C), RS1003852181 (12:53998409 G>C), RS1004594771 (12:53998847 T>C), RS1004946065 (12:53999199 G>A), RS1005594873 (12:54001386 G>A), RS1005614969 (12:54001846 C>A)

Disease associations

OMIM: gene MIM:142971 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST005956_70	Waist-to-hip ratio adjusted for BMI	4.000000e-13
GCST005957_6	Waist-to-hip ratio adjusted for BMI (age <50)	6.000000e-06
GCST005958_9	Waist-to-hip ratio adjusted for BMI (age >50)	1.000000e-08
GCST005962_20	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	7.000000e-13
GCST006979_1060	Heel bone mineral density	4.000000e-15
GCST012228_550	Waist-hip index	7.000000e-12
GCST012230_44	Waist-to-hip ratio adjusted for BMI	2.000000e-11
GCST90020024_226	A body shape index	5.000000e-10
GCST90020024_227	A body shape index	4.000000e-09
GCST90020024_275	A body shape index	6.000000e-40
GCST90020025_86	Waist-to-hip ratio adjusted for BMI	1.000000e-31
GCST90020025_87	Waist-to-hip ratio adjusted for BMI	3.000000e-09
GCST90020027_1665	Waist-hip index	6.000000e-33
GCST90020027_1666	Waist-hip index	4.000000e-09
GCST90020029_456	Waist circumference adjusted for body mass index	5.000000e-37
GCST90020029_457	Waist circumference adjusted for body mass index	3.000000e-10

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0009270	heel bone mineral density
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, decreases methylation, increases expression, affects response to substance	3
Cadmium	increases abundance, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
bisphenol A	affects cotreatment, increases methylation	1
arsenite	increases methylation	1
potassium chromate(VI)	increases expression	1
nickel sulfate	increases expression	1
ICG 001	increases expression	1
MRK 003	decreases expression	1
(+)-JQ1 compound	decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Temozolomide	increases expression	1
Arsenic Trioxide	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Nickel	decreases expression	1
Tretinoin	increases expression	1
Triclosan	increases expression	1
Tunicamycin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Thapsigargin	decreases expression	1
Copper Sulfate	decreases 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_A3A2	SEES3-1V human HOXC9, clone1	Embryonic stem cell	Male
CVCL_A3A3	SEES3-1V human HOXC9, clone2	Embryonic stem cell	Male
CVCL_A3A4	SEES3-1V human HOXC9, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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