KLF9

Summary

KLF9 (KLF transcription factor 9, HGNC:1123) is a protein-coding gene on chromosome 9q21.12, encoding Krueppel-like factor 9 (Q13886). Transcription factor that binds to GC box promoter elements.

The protein encoded by this gene is a transcription factor that binds to GC box elements located in the promoter. Binding of the encoded protein to a single GC box inhibits mRNA expression while binding to tandemly repeated GC box elements activates transcription.

Source: NCBI Gene 687 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 18 total
• Transcription factor: yes — 27 downstream targets (CollecTRI)
• MANE Select transcript: NM_001206

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1123
Approved symbol	KLF9
Name	KLF transcription factor 9
Location	9q21.12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000119138
Ensembl biotype	protein_coding
OMIM	602902
Entrez	687

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000377126

RefSeq mRNA: 1 — MANE Select: NM_001206 NM_001206

CCDS: CCDS6633

Canonical transcript exons

ENST00000377126 — 2 exons

Exon	Start	End
ENSE00001472854	70384604	70388005
ENSE00001472857	70412859	70414657

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 98.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.6500 / max 100.8558, expressed in 1500 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100854	4.3469	1203
100840	3.3031	1158

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	98.55	gold quality
paraflocculus	UBERON:0005351	98.28	gold quality
buccal mucosa cell	CL:0002336	98.18	gold quality
lower lobe of lung	UBERON:0008949	98.08	gold quality
right lung	UBERON:0002167	98.00	gold quality
mucosa of stomach	UBERON:0001199	97.60	gold quality
synovial joint	UBERON:0002217	97.51	gold quality
cerebellar vermis	UBERON:0004720	97.18	gold quality
tibial artery	UBERON:0007610	96.86	gold quality
popliteal artery	UBERON:0002250	96.85	gold quality
tibial nerve	UBERON:0001323	96.80	gold quality
vena cava	UBERON:0004087	96.53	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.53	gold quality
left uterine tube	UBERON:0001303	96.48	gold quality
gastrocnemius	UBERON:0001388	96.45	gold quality
muscle of leg	UBERON:0001383	96.14	gold quality
saphenous vein	UBERON:0007318	96.14	gold quality
diaphragm	UBERON:0001103	96.12	gold quality
pericardium	UBERON:0002407	96.08	gold quality
aorta	UBERON:0000947	96.01	gold quality
muscle organ	UBERON:0001630	95.85	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	95.59	gold quality
vastus lateralis	UBERON:0001379	95.54	gold quality
frontal pole	UBERON:0002795	95.46	gold quality
subcutaneous adipose tissue	UBERON:0002190	95.34	gold quality
quadriceps femoris	UBERON:0001377	95.30	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.20	gold quality
urethra	UBERON:0000057	95.16	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.16	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	95.13	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	34.59
E-ANND-3	yes	26.42
E-GEOD-84465	yes	6.89

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

27 targets.

Target	Regulation
AXL
C1QTNF12	Unknown
CDKN1A	Activation
CEBPB	Unknown
CYP11A1
CYP1A1	Repression
CYP7A1	Activation
DIO1	Unknown
DKK1	Unknown
EEF1A1	Activation
FGFR1	Activation
IGFBP2	Activation
LDLR	Activation
MAPK8
MYH10
MYH11
NOTCH1
PDCD5	Activation
PGR	Unknown
PMAIP1	Repression
PPARG	Unknown
ROS1
SLPI	Unknown
STAR
TBXT
TFAP2A
TXNRD2

JASPAR motifs

Motif	Name	Family
MA1107.1	KLF9	Three-zinc finger Kruppel-related
MA1107.2	KLF9	Three-zinc finger Kruppel-related
MA1107.3	KLF9	Three-zinc finger Kruppel-related

JASPAR matrix evidence (PMIDs): PMID:12620113

Upstream regulators (CollecTRI, top): CEBPD, HOXA10, NR3C1

miRNA regulators (miRDB)

218 targeting KLF9, 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-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775

Literature-anchored findings (GeneRIF, showing 40)

• BTEB1/Progesterone receptor cross-talk to facilitate progesterone dependent gene transcription in endometrial epithelial cells. (PMID:16384861)
• identify KLF9 as a transcriptional repressor of estrogen receptor alpha signaling (PMID:17717078)
• Transient transfection of Kruppel-like factor 9 suppressed LDLR, steroidogenic acute regulatory protein, and CYP11A (PMID:18056793)
• KLF9 did not reveal a otosclerosis-causing mutation (PMID:18224337)
• HNF4alpha regulates thyroid hormone homeostasis through transcriptional regulation of the Dio1 gene with GATA4 and KLF9 (PMID:18426912)
• KLF9 may be involved in the carcinogenesis of human colorectal cancer. (PMID:18477211)
• KLF9 influences the expression of uterine epithelial genes through mechanisms likely involving its transcriptional activator and repressor functions and which may underlie altered tumor biology with aberrant KLF9 expression. (PMID:18783612)
• T3-induced genes identified basic transcription element binding protein 1/Kruppel-like factor 9 (BTEB1/KLF9) and GAR22 as TR target genes (PMID:19375645)
• Data support cross-regulation among BMP2, KLF9, and KLF13 to maintain progesterone sensitivity in stromal cells undergoing differentiation and suggest that loss of this network compromises establishment of uterine receptivity and implantation success. (PMID:20410205)
• homeobox A10(HOXA10) directly and selectively repressed Kruppel-like factor 9 expression in endometrial epithelial cells (PMID:20463357)
• these results show for the first time that KLF9 has differentiating and tumor-suppressing functions in tumor-initiating stem cells. (PMID:21280156)
• It was suggested that KLF9 loss-of-expression accompanying endometrial carcinogenesis may predispose endometrial epithelial cells to mechanisms of escape from estrogen-mediated growth regulation, leading to progression of established neoplasms. (PMID:21543766)
• Expression levels of HOXA11, LIF and BTEB1 mRNA were measured in endometrium during the mid-secretory phase using semi-quantitative RT-PCR (PMID:21987111)
• Data identify KLF9 as a novel and potentially clinically relevant transcriptional regulator of drug-induced apoptosis in multiple myeloma cells. (PMID:22144178)
• Loss of KLF9 coregulation of endometrial stromal progesterone receptor-responsive gene networks may underlie progesterone resistance in endometriosis. (PMID:22259059)
• Klf9 affects keratinocyte proliferation/differentiation by controlling the expression of target genes in a daytime-dependent manner. (PMID:22711835)
• Studied mRNA levels of FOXO1, KLF9 and YT521 in human normal and cancerous endometrial tissue. In subjects with endometrial cancer the KLF9 mRNA level (1.12 +/- 0.38) was lower (p < 0.001) when compared to controls (3.11 +/- 1.52). (PMID:23865345)
• We confirmed that PDCD5 overexpression stimulated the promoter activities of KLF9 by luciferase reporter assays. (PMID:24173774)
• Nrf2 amplifies oxidative stress via induction of Klf9. (PMID:24613345)
• Data collectively show that KLF9 substantially inhibits AKT activation and abrogates tumor growth of PCa cells. (PMID:24737412)
• the expression of KLF9 is up-regulated in human ovarian cancer; KLF9 knockdown significantly inhibited cell proliferation and resulted in cell cycle arrest in the G0/G1 phase (PMID:25216959)
• increased KLF9 expression is in part responsible for CYP2D6 induction during pregnancy via the potentiation of HNF4alpha transactivation of CYP2D6. (PMID:25217496)
• KLF9 suppresses the growth of hepatocellular carcinoma cells in vivo and positively regulates p53 expression by increasing protein stability. (PMID:25242357)
• Data indicate that integrin alpha6 repression by Kruppel-like factor-9 (KLF9) inhibits glioblastoma cell stemness and tumorigenicity. (PMID:25288800)
• Reduced KLF9 expression is associated with glioma. (PMID:25305446)
• Myometrial KLF9 may contribute to the onset of human parturition through its regulation of PGR expression and inflammatory signaling networks. (PMID:25313913)
• TRs cooperate with KLF9 to regulate hepatocyte proliferation and differentiation and early stages of organogenesis and that TRs exert widespread and important influences on ESC biology. (PMID:25330987)
• The expression of KLF9 is down-regulated in esophageal squamous cell carcinoma and inversely correlated with the clinical features. (PMID:25641762)
• In this review, we focus on the functions, roles, and regulatory networks of these five KLFs in HCC, summarize key pathways, and propose areas for further investigation (PMID:25652467)
• Palmitic acid increases Ppargamma and Klf6 & Klf9 gene expression and promotes triglyceride accumulation in HepG2 cells. (PMID:25686501)
• Suggest role for miR-570/KLF9 molecular network in controlling lung carcinoma progression. (PMID:26045791)
• miR-141-3p/KLF9 may play an important role in regulating the growth of prostate cancer (PMID:27956179)
• KLF9 status was associated with differentiation and vascular invasion expression and was found to be a valuable prognostic factor for patients with pancreatic ductal adenocarcinoma (PMID:28668877)
• In conclusion, LPA plays dual roles as a ligand mediator through the activation of cell surface G-coupled protein receptors and as an intracellular second messenger through the activation of PPARgamma. We discuss the contribution of the LPA1-PPARgamma-KLF9 axis to neurite outgrowth and proliferation in human iPSC-derived neurons. (PMID:28716732)
• KLF9 could down-regulate MMP9 expression to inhibit breast cancer metastasis. (PMID:29107105)
• results demonstrated the molecular interaction between miR-378 and KLF9, indicating the therapeutic potential of miR-378 for osteosarcoma. (PMID:29490146)
• KLF9 suppressed tumorigenicity of the pancreatic ductal adenocarcinoma by negatively regulating frizzled-5. (PMID:29621541)
• XBP1s transcriptionally activates KLF9 under conditions of high ER stress. (PMID:30282030)
• KLF9 and BCL3 as transcription factors that enhance reprogramming of primordial germ cells (PMID:30286177)
• Low KLF9 expression is associated with proliferation and invasion of glioma. (PMID:30431124)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	klf9	ENSDARG00000068194
mus_musculus	Klf9	ENSMUSG00000033863
rattus_norvegicus	Klf9	ENSRNOG00000014215
drosophila_melanogaster	luna	FBGN0040765

Paralogs (22): KLF6 (ENSG00000067082), KLF8 (ENSG00000102349), KLF5 (ENSG00000102554), KLF1 (ENSG00000105610), KLF3 (ENSG00000109787), KLF7 (ENSG00000118263), KLF12 (ENSG00000118922), KLF2 (ENSG00000127528), KLF16 (ENSG00000129911), KLF4 (ENSG00000136826), KLF10 (ENSG00000155090), KLF15 (ENSG00000163884), SP8 (ENSG00000164651), KLF13 (ENSG00000169926), SP7 (ENSG00000170374), KLF17 (ENSG00000171872), KLF11 (ENSG00000172059), SP6 (ENSG00000189120), SP5 (ENSG00000204335), SP9 (ENSG00000217236), KLF14 (ENSG00000266265), KLF18 (ENSG00000283039)

Protein

Protein identifiers

Krueppel-like factor 9 — Q13886 (reviewed: Q13886)

Alternative names: Basic transcription element-binding protein 1, GC-box-binding protein 1, Transcription factor BTEB1

All UniProt accessions (1): Q13886

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that binds to GC box promoter elements. Selectively activates mRNA synthesis from genes containing tandem repeats of GC boxes but represses genes with a single GC box. Acts as an epidermal circadian transcription factor regulating keratinocyte proliferation.

Subunit / interactions. Interacts with ZZEF1.

Subcellular location. Nucleus.

Tissue specificity. Epidermis (at protein level).

Induction. Expression is highly sensitive to glucocorticoids and shows diurnal expression patterns. A strong induction of expression seen during keratinocyte differentiation in a cortisol dependent manner.

Similarity. Belongs to the Sp1 C2H2-type zinc-finger protein family.

RefSeq proteins (1): NP_001197* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (6 total): zinc finger region 3, chain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13886-F1	63.69	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): 122

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9764790	Positive Regulation of CDH1 Gene Transcription

MSigDB gene sets: 0 (showing top):

GO Biological Process (5): regulation of transcription by RNA polymerase II (GO:0006357), circadian rhythm (GO:0007623), negative regulation of keratinocyte proliferation (GO:0010839), cellular response to cortisol stimulus (GO:0071387), rhythmic process (GO:0048511)

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), zinc ion binding (GO:0008270), DNA binding (GO:0003677), metal ion binding (GO:0046872)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), plasma membrane (GO:0005886)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Regulation of CDH1 Gene Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
rhythmic process	1
regulation of keratinocyte proliferation	1
keratinocyte proliferation	1
negative regulation of epithelial cell proliferation	1
response to cortisol	1
cellular response to glucocorticoid stimulus	1
cellular response to alcohol	1
cellular response to ketone	1
biological_process	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
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1588 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KLF9	PGR	P06401	859
KLF9	SIN3A	Q96ST3	850
KLF9	TRPM3	Q9HCF6	667
KLF9	FKBP5	Q13451	597
KLF9	JUN	P05412	505
KLF9	KLF6	Q99612	501
KLF9	IGFBP1	P08833	476
KLF9	TBX3	O15119	467
KLF9	TFAP2A	P05549	466
KLF9	TXNIP	Q9H3M7	461
KLF9	EEF1A1	P04719	454
KLF9	JUND	P17535	452
KLF9	CYP3A7	P24462	449
KLF9	CYP1A1	P04798	441
KLF9	GATA1	P15976	433

IntAct

4 interactions, top by confidence:

A	B	Type	Score
PGR	KLF9	psi-mi:“MI:0915”(physical association)	0.400
KLF9	TPM3	psi-mi:“MI:0914”(association)	0.350
KLF9	SEC16A	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (99): KLF9 (Two-hybrid), PGR (Affinity Capture-Western), TP53 (Co-localization), SIN3A (Reconstituted Complex), KLF9 (Positive Genetic), KLF9 (Affinity Capture-RNA), SIN3A (Proximity Label-MS), SIN3B (Proximity Label-MS), GABPA (Proximity Label-MS), MGA (Proximity Label-MS), BBX (Proximity Label-MS), BAZ1B (Proximity Label-MS), NR2C2 (Proximity Label-MS), PBRM1 (Proximity Label-MS), HIVEP1 (Proximity Label-MS)

ESM2 similar proteins: A0A068A9T3, A0A084AFG9, A0A1U8QIH0, A0A2R6S148, A0A345BJN6, A0A3G1DJG8, A0A443HK05, A0A481WNP6, A0A4D6Q411, A0A4D6Q4S0, A0A4D6QCQ2, A0A6S6AAU0, F1B281, G0KYB3, G4MM89, G4NDH1, I1RF54, K3VZ28, M1ETK3, M1W424, O35739, P15315, P32805, P49953, P50902, P79288, P9WEF9, P9WF00, Q01713, Q03081, Q0CE14, Q13886, Q22678, Q2UA42, Q2V3L3, Q32PH1, Q4KM91, Q567C6, Q5B7I6, Q5B7I8

Diamond homologs: A6QQW0, B4F7E9, O70230, P36508, P52747, P79288, Q13886, Q1LYE3, Q58DZ6, Q5XIU2, Q8BMU0, Q91853, O08584, O35738, O35739, O35819, O43474, O62259, O75840, O89090, O95600, P08047, P0CG40, P46099, P57682, P58334, Q01713, Q01714, Q02446, Q0VA40, Q13887, Q14V87, Q19A40, Q5XGT8, Q60793, Q60843, Q60980, Q62445, Q64HY3, Q64HY5

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
NR3C1	“up-regulates quantity by expression”	KLF9	“transcriptional regulation”
KLF9	“up-regulates activity”	SIN3A	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

310 predictions. Top by Δscore:

Variant	Effect	Δscore
9:70388003:CAC:C	acceptor_gain	1.0000
9:70388004:ACCTA:A	acceptor_loss	1.0000
9:70388005:CCTA:C	acceptor_loss	1.0000
9:70388006:CT:C	acceptor_loss	1.0000
9:70388001:TTCAC:T	acceptor_gain	0.9900
9:70388002:TCAC:T	acceptor_gain	0.9900
9:70388003:CACC:C	acceptor_gain	0.9900
9:70388004:AC:A	acceptor_gain	0.9900
9:70388005:CC:C	acceptor_gain	0.9900
9:70388006:C:CC	acceptor_gain	0.9900
9:70388006:C:T	acceptor_gain	0.9400
9:70412910:T:A	donor_gain	0.9400
9:70412504:T:TA	donor_gain	0.9300
9:70412505:C:A	donor_gain	0.9300
9:70413104:T:A	donor_gain	0.9200
9:70388004:ACCT:A	acceptor_gain	0.9100
9:70414400:T:TA	donor_gain	0.9000
9:70388002:TCACC:T	acceptor_gain	0.8900
9:70388006:C:A	acceptor_gain	0.8500
9:70411141:AG:A	donor_gain	0.8300
9:70413049:CG:C	donor_gain	0.8200
9:70388003:CACCT:C	acceptor_gain	0.8100
9:70388005:CCT:C	acceptor_gain	0.8000
9:70411142:G:C	donor_gain	0.8000
9:70413095:T:C	donor_gain	0.8000
9:70412494:C:CA	donor_gain	0.7900
9:70388021:C:CT	acceptor_gain	0.7800
9:70388007:T:A	acceptor_gain	0.7700
9:70414367:T:TA	donor_gain	0.7600
9:70411821:T:C	donor_gain	0.7500

AlphaMissense

1600 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:70387875:G:C	F212L	1.000
9:70387875:G:T	F212L	1.000
9:70387877:A:G	F212L	1.000
9:70387898:A:G	C205R	1.000
9:70387920:G:C	H197Q	1.000
9:70387920:G:T	H197Q	1.000
9:70387942:A:G	L190P	1.000
9:70387959:G:C	F184L	1.000
9:70387959:G:T	F184L	1.000
9:70387961:A:G	F184L	1.000
9:70387971:G:C	C180W	1.000
9:70387986:G:C	C175W	1.000
9:70387988:A:G	C175R	1.000
9:70387836:G:C	H225Q	0.999
9:70387836:G:T	H225Q	0.999
9:70387848:G:C	H221Q	0.999
9:70387848:G:T	H221Q	0.999
9:70387858:A:G	L218P	0.999
9:70387876:A:G	F212S	0.999
9:70387887:A:C	C208W	0.999
9:70387888:C:G	C208S	0.999
9:70387888:C:T	C208Y	0.999
9:70387889:A:G	C208R	0.999
9:70387889:A:T	C208S	0.999
9:70387902:G:C	F203L	0.999
9:70387902:G:T	F203L	0.999
9:70387904:A:G	F203L	0.999
9:70387922:G:C	H197D	0.999
9:70387927:C:G	R195P	0.999
9:70387932:G:C	H193Q	0.999

dbSNP variants (sampled 300 via entrez): RS1000023143 (9:70386642 T>C), RS1000048041 (9:70393893 T>A,C), RS1000152466 (9:70393507 C>A,T), RS1000266109 (9:70400472 G>A), RS1000312031 (9:70387163 G>A), RS1000326237 (9:70408023 C>G,T), RS1000442407 (9:70407743 A>G), RS1000664631 (9:70406359 C>T), RS1000709333 (9:70387588 A>T), RS1000720918 (9:70400753 G>A), RS1000778842 (9:70405975 G>A), RS1000927231 (9:70398492 T>A), RS1001077664 (9:70392334 T>C), RS1001165244 (9:70395140 G>A), RS1001197456 (9:70406329 C>G,T)

Disease associations

OMIM: gene MIM:602902 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001416_6	Body mass index (SNP x SNP interaction)	1.000000e-09
GCST002461_22	Body mass index	3.000000e-08
GCST005316_57	Intelligence (MTAG)	3.000000e-08
GCST006069_67	Time-dependent creatinine clearance change response to tenofovir treatment in HIV infection (time and treatment arm interaction)	9.000000e-06
GCST006979_163	Heel bone mineral density	8.000000e-11
GCST009391_757	Metabolite levels	9.000000e-06
GCST009676_8	Urinary calcium excretion	8.000000e-07
GCST010002_320	Refractive error	3.000000e-39
GCST012299_13	Schizophrenia, bipolar disorder or major depressive disorder x sex interaction (3df)	9.000000e-06

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004337	intelligence
EFO:0007934	creatinine clearance measurement
EFO:0009270	heel bone mineral density
EFO:0010390	sphingomyelin 14:0 measurement
EFO:0004838	calcium measurement
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases methylation	9
bisphenol A	increases methylation, affects cotreatment, increases expression, affects expression, decreases expression (+1 more)	4
Triiodothyronine	decreases expression, increases expression	4
Arsenic Trioxide	decreases expression, decreases reaction, affects cotreatment, increases expression	3
sodium arsenite	decreases expression	2
entinostat	increases expression, affects cotreatment	2
Air Pollutants	decreases expression, increases abundance	2
Benzo(a)pyrene	decreases expression, affects methylation	2
Estradiol	affects cotreatment, decreases expression, increases expression	2
Methylcholanthrene	decreases expression, affects binding, increases reaction	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
Tretinoin	affects cotreatment, increases expression, decreases expression	2
Tunicamycin	increases expression	2
Cyclosporine	decreases expression, increases expression	2
Cadmium Chloride	decreases expression, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
Particulate Matter	affects cotreatment, decreases expression, increases abundance	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	increases expression	1
TAK-243	increases sumoylation	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
allicin	decreases expression, decreases reaction	1
trichostatin A	increases expression	1
beta-lapachone	increases expression	1
zinc chromate	increases abundance, increases expression	1
manganese chloride	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1

Cellosaurus cell lines

5 cell lines: 3 embryonic stem cell, 1 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A3S3	SEES3-1V human KLF9, clone1	Embryonic stem cell	Male
CVCL_A3S4	SEES3-1V human KLF9, clone2	Embryonic stem cell	Male
CVCL_A3S5	SEES3-1V human KLF9, clone3	Embryonic stem cell	Male
CVCL_HA18	MCF-7 eGFP-KLF9	Cancer cell line	Female
CVCL_HC83	HEK293 eGFP-KLF9	Transformed cell line	Female

Clinical trials (associated diseases)

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