LMO1

Summary

LMO1 (LIM domain only 1, HGNC:6641) is a protein-coding gene on chromosome 11p15.4, encoding Rhombotin-1 (P25800). May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.

This locus encodes a transcriptional regulator that contains two cysteine-rich LIM domains but lacks a DNA-binding domain. LIM domains may play a role in protein interactions; thus the encoded protein may regulate transcription by competitively binding to specific DNA-binding transcription factors. Alterations at this locus have been associated with acute lymphoblastic T-cell leukemia. Chromosomal rearrangements have been observed between this locus and at least two loci, the delta subunit of the T-cell antigen receptor gene and the LIM domain binding 1 gene. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 4004 — RefSeq curated summary.

At a glance

• GWAS associations: 21
• Clinical variants (ClinVar): 23 total
• Phenotypes (HPO): 34
• MANE Select transcript: NM_002315

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6641
Approved symbol	LMO1
Name	LIM domain only 1
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Aliases	TTG1, RHOM1
Ensembl gene	ENSG00000166407
Ensembl biotype	protein_coding
OMIM	186921
Entrez	4004

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000335790, ENST00000428101, ENST00000524379, ENST00000534484, ENST00000963877

RefSeq mRNA: 2 — MANE Select: NM_002315 NM_001270428, NM_002315

CCDS: CCDS44534, CCDS58118

Canonical transcript exons

ENST00000335790 — 4 exons

Exon	Start	End
ENSE00001102688	8226975	8227100
ENSE00002163839	8224309	8224721
ENSE00002169065	8263338	8263878
ENSE00003597580	8230291	8230504

Expression profiles

Bgee: expression breadth ubiquitous, 150 present calls, max score 86.64.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3528 / max 53.8554, expressed in 123 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
118494	0.1968	71
118493	0.0986	38
118495	0.0336	17
118492	0.0123	4
118496	0.0114	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.64	gold quality
vastus lateralis	UBERON:0001379	86.20	silver quality
hindlimb stylopod muscle	UBERON:0004252	85.99	gold quality
oocyte	CL:0000023	85.32	gold quality
quadriceps femoris	UBERON:0001377	84.63	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.73	gold quality
pigmented layer of retina	UBERON:0001782	83.72	gold quality
secondary oocyte	CL:0000655	82.14	gold quality
biceps brachii	UBERON:0001507	82.10	gold quality
islet of Langerhans	UBERON:0000006	81.22	gold quality
muscle organ	UBERON:0001630	81.10	gold quality
gastrocnemius	UBERON:0001388	80.63	gold quality
muscle of leg	UBERON:0001383	80.47	gold quality
type B pancreatic cell	CL:0000169	80.18	gold quality
skeletal muscle tissue	UBERON:0001134	79.62	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	79.32	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	79.05	silver quality
ganglionic eminence	UBERON:0004023	76.57	gold quality
diaphragm	UBERON:0001103	76.02	gold quality
skin of abdomen	UBERON:0001416	75.63	gold quality
muscle tissue	UBERON:0002385	74.18	gold quality
skin of leg	UBERON:0001511	73.21	gold quality
gluteal muscle	UBERON:0002000	72.58	gold quality
zone of skin	UBERON:0000014	72.51	gold quality
hypothalamus	UBERON:0001898	69.65	gold quality
ventricular zone	UBERON:0003053	69.55	gold quality
deltoid	UBERON:0001476	69.25	silver quality
prefrontal cortex	UBERON:0000451	68.48	gold quality
olfactory bulb	UBERON:0002264	67.09	gold quality
pancreatic ductal cell	CL:0002079	66.63	silver quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-6524	yes	186.69
E-MTAB-5061	yes	14.48
E-GEOD-93593	yes	10.73
E-MTAB-9388	yes	5.99
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
NKX3-1

Upstream regulators (CollecTRI, top): ARX, E2F1, EGR1, ETS2, GATA3, LMO2, MYBL2, SHOX2, TAL1

miRNA regulators (miRDB)

26 targeting LMO1, 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-4262	100.00	73.26	3931
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-4755-3P	98.77	65.59	1915
HSA-MIR-6880-5P	98.08	65.59	1282
HSA-MIR-6842-3P	98.07	66.33	1325
HSA-MIR-874-5P	96.93	63.92	1014
HSA-MIR-642B-5P	96.37	67.26	745
HSA-MIR-541-3P	96.07	66.11	1271
HSA-MIR-654-5P	96.07	66.18	1280
HSA-MIR-3131	95.33	65.74	102
HSA-MIR-5092	93.86	62.63	151
HSA-MIR-611	93.79	64.24	81

Literature-anchored findings (GeneRIF, showing 18)

• 60% of transgenic mice that overexpressed both OLIG2 and LMO1 developed pre-T lymphoblastic lymphoma/leukemia with large thymic tumor masses. (PMID:16103065)
• The present data suggest that TGF-beta, LMO1, possibly RUNX3, and GSDM form a regulatory pathway for directing the pit cells to apoptosis. (PMID:17471240)
• data show that common polymorphisms at the LMO1 locus are strongly associated with susceptibility to developing neuroblastoma, but also may influence the likelihood of further somatic alterations at this locus, leading to malignant progression (PMID:21124317)
• genetic variants within LMO1 are associated with acute lymphoblastic leukemia and identify this gene as a strong candidate for precursor B-cell leukemogenesis. (PMID:21602560)
• results show that LMO1 is poised for expression in normal progenitors, where activation of SCL/TAL1 together with a breakdown of epigenetic repression of LMO1 regulatory elements (PMID:23302769)
• LMO1 is a commonly activated tumor promoter that activates AKT signaling in colorectal cancer and a new predictive marker for targeted therapy. (PMID:24845030)
• LMO1 is a commonly activated tumor promoter that activates AKT signaling in non-small cell lung cancer. (PMID:25037573)
• data suggest that genetic variants in LMO1 are associated with increased NB risk in Chinese children. (PMID:26030754)
• LMO1 appears to be a coactivator of AR involved in the progression of prostate cancer (PMID:26459575)
• a polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis (PMID:26560027)
• These results suggested that LMO1 gene rs110419 A > G polymorphism may contribute to protection against neuroblastoma (PMID:27009839)
• A C-to-T single nucleotide transition occurs as a somatic mutation in noncoding sequences 4 kb upstream of the transcriptional start site of the LMO1 oncogene in primary samples from patients with T-cell acute lymphoblastic leukaemia. This conforms to an APOBEC-like cytidine deaminase mutational signature and a new MYB binding site driving high levels of LMO1 expression. (PMID:28260788)
• IKZF1 rs10235796 C allele, IKZF1 rs6964969A>G, CDKN2A rs3731246 G>C, and CDKN2A rs3731246 C allele were signi fi cantly associated with Acute Lymphoblastic Leukemia in Yemenis of Arab-Asian descent. Borderline association found in IKZF1 rs4132601 T>G variant. No associations found with LMO1 rs442264; rs3794012; rs4237770 (PMID:28768142)
• LMO1 is an important oncogene that promotes neuroblastoma initiation, progression, and widespread metastatic dissemination. (PMID:28867147)
• Target genes of the LMO1-regulated microRNAs and their relevant pathways may be a potential therapeutic targe (PMID:30194082)
• ASCL1 and LMO1 directly regulate the expression of CRC genes, indicating that ASCL1 is a member and LMO1 is a coregulator of the ADRN neuroblastoma core regulatory circuitry. (PMID:31819055)
• LMO1 polymorphisms and the risk of neuroblastoma: Assessment of meta-analysis of case-control studies. (PMID:31830377)
• Circ_0021087 acts as a miR-184 sponge and represses gastric cancer progression by adsorbing miR-184 and elevating FOSB expression. (PMID:34076278)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lmo1	ENSDARG00000034504
mus_musculus	Lmo1	ENSMUSG00000036111
rattus_norvegicus	Lmo1	ENSRNOG00000014629

Paralogs (20): FHL1 (ENSG00000022267), LMO3 (ENSG00000048540), LHX5 (ENSG00000089116), ZFHX4 (ENSG00000091656), LHX2 (ENSG00000106689), LHX6 (ENSG00000106852), LHX3 (ENSG00000107187), LHX4 (ENSG00000121454), LMO2 (ENSG00000135363), ZFHX2 (ENSG00000136367), LMX1B (ENSG00000136944), ZFHX3 (ENSG00000140836), LMO4 (ENSG00000143013), LHX9 (ENSG00000143355), CRIP3 (ENSG00000146215), LHX8 (ENSG00000162624), LMX1A (ENSG00000162761), CRIP2 (ENSG00000182809), CRIP1 (ENSG00000213145), LHX1 (ENSG00000273706)

Protein

Protein identifiers

Rhombotin-1 — P25800 (reviewed: P25800)

Alternative names: Cysteine-rich protein TTG-1, LIM domain only protein 1, T-cell translocation protein 1

All UniProt accessions (2): E9PK83, P25800

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.

Subcellular location. Nucleus.

Tissue specificity. Expressed mainly in the central nervous. Low level of expression in other tissues including thymus.

Disease relevance. A chromosomal aberration involving LMO1 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(11,14)(p15;q11) with TCRD.

Isoforms (2)

UniProt ID	Names	Canonical?
P25800-1	1	yes
P25800-2	2

RefSeq proteins (2): NP_001257357, NP_002306* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001781	Znf_LIM	Domain
IPR050945	LMO_RBTN_TF	Family

Pfam: PF00412

UniProt features (4 total): domain 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P25800-F1	88.15	0.71

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs

MSigDB gene sets: 228 (showing top): MORF_RAGE, GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_LEUKOCYTE_PROLIFERATION, BENPORATH_ES_WITH_H3K27ME3, CCAWYNNGAAR_UNKNOWN, GOBP_T_CELL_HOMEOSTASIS, GOBP_LYMPHOCYTE_HOMEOSTASIS, CHX10_01, AACWWCAANK_UNKNOWN, NKX61_01, GOBP_LEUKOCYTE_PROLIFERATION, GATA3_01, OCT1_03, KMCATNNWGGA_UNKNOWN, OCT1_06

GO Biological Process (3): negative regulation of transcription by RNA polymerase II (GO:0000122), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of T cell homeostatic proliferation (GO:0046013)

GO Molecular Function (4): transcription coactivator activity (GO:0003713), metal ion binding (GO:0046872), DNA-binding transcription factor binding (GO:0140297), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Transcriptional regulation by RUNX1	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
positive regulation of DNA-templated transcription	2
negative regulation of DNA-templated transcription	1
T cell homeostatic proliferation	1
regulation of T cell proliferation	1
transcription coregulator activity	1
cation binding	1
transcription factor binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1074 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LMO1	LDB1	Q86U70	973
LMO1	LDB2	O43679	922
LMO1	TAL1	P17542	876
LMO1	TAL2	Q16559	863
LMO1	LYL1	P12980	857
LMO1	TLX1	P31314	817
LMO1	TLX3	O43711	807
LMO1	CRIP1	P50238	774
LMO1	CSRP1	P21291	717
LMO1	TCF3	P15883	708
LMO1	GSDMA	Q96QA5	696
LMO1	GATA1	P15976	689
LMO1	TES	Q9UGI8	685
LMO1	DENND2B	P78523	684
LMO1	ARIH2	O95376	682

IntAct

425 interactions, top by confidence:

A	B	Type	Score
ZBTB43	LMO1	psi-mi:“MI:0915”(physical association)	0.830
LMO1	ZBTB43	psi-mi:“MI:0915”(physical association)	0.830
LMO1	BLZF1	psi-mi:“MI:0915”(physical association)	0.780
TFIP11	LMO1	psi-mi:“MI:0915”(physical association)	0.780
BLZF1	LMO1	psi-mi:“MI:0915”(physical association)	0.780
LMO1	TFIP11	psi-mi:“MI:0915”(physical association)	0.780
LMO1	LPXN	psi-mi:“MI:0915”(physical association)	0.740
PTPN3	LMO1	psi-mi:“MI:0915”(physical association)	0.720
GOLGA2	LMO1	psi-mi:“MI:0915”(physical association)	0.720
KANK2	LMO1	psi-mi:“MI:0915”(physical association)	0.720
LMO1	GOLGA2	psi-mi:“MI:0915”(physical association)	0.720
LMO1	KANK2	psi-mi:“MI:0915”(physical association)	0.720
LMO1	PTPN3	psi-mi:“MI:0915”(physical association)	0.720
LMO1	NAGK	psi-mi:“MI:0915”(physical association)	0.700
GABPB1	LMO1	psi-mi:“MI:0915”(physical association)	0.670
LMO1	LDB1	psi-mi:“MI:0915”(physical association)	0.670
LMO1	IKZF3	psi-mi:“MI:0915”(physical association)	0.670
LDB1	LMO1	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (171): LMO1 (Two-hybrid), LMO1 (Two-hybrid), LMO1 (Two-hybrid), LMO1 (Two-hybrid), LMO1 (Two-hybrid), PTPN3 (Two-hybrid), RBBP8 (Two-hybrid), REL (Two-hybrid), TRIM27 (Two-hybrid), SOX5 (Two-hybrid), TCF4 (Two-hybrid), BLZF1 (Two-hybrid), LDB1 (Two-hybrid), LPXN (Two-hybrid), IKZF3 (Two-hybrid)

ESM2 similar proteins: A0A324, A1XQR9, A4FUI2, A5JSS2, A6MZM2, G1SHQ2, O09167, O14602, O35900, O60739, P20280, P25800, P41567, P46778, P47813, P48024, P49666, P51971, P61220, P62303, P62304, P62305, P62308, P62309, Q09028, Q0D5W6, Q0P5B3, Q2KIA3, Q3B8H4, Q3ZBL0, Q4R4X9, Q503U0, Q5E938, Q5RA42, Q5RBW7, Q5RFF4, Q60872, Q60972, Q6GVM3, Q6QN05

Diamond homologs: A0JNI8, A2I8Z7, A2PZF9, G5EC36, G5EE86, O14639, O35652, O60663, O88609, O94929, O97581, P20154, P25791, P25800, P25801, P29673, P29674, P34764, P34765, P36198, P36200, P37137, P48742, P50211, P50212, P50458, P50480, P50481, P52889, P53405, P53406, P53407, P53408, P53409, P53410, P53411, P53412, P53413, P53667, P53668

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
LMO1	up-regulates	TAL1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1342 predictions. Top by Δscore:

Variant	Effect	Δscore
11:8226970:CTGA:C	donor_loss	1.0000
11:8226971:TGA:T	donor_loss	1.0000
11:8226972:GA:G	donor_loss	1.0000
11:8226974:C:CT	donor_loss	1.0000
11:8226974:CCT:C	donor_gain	1.0000
11:8227100:CCT:C	acceptor_loss	1.0000
11:8228225:C:CA	donor_gain	1.0000
11:8227096:AGAGC:A	acceptor_gain	0.9900
11:8227097:GAGC:G	acceptor_gain	0.9900
11:8227099:GC:G	acceptor_gain	0.9900
11:8227100:CC:C	acceptor_gain	0.9900
11:8227101:C:CC	acceptor_gain	0.9900
11:8227106:G:T	acceptor_gain	0.9900
11:8230285:GCCCA:G	donor_loss	0.9900
11:8230286:CCCA:C	donor_loss	0.9900
11:8230287:CCACC:C	donor_loss	0.9900
11:8230288:CA:C	donor_loss	0.9900
11:8230290:C:G	donor_loss	0.9900
11:8230500:CACGC:C	acceptor_gain	0.9900
11:8230502:CGC:C	acceptor_gain	0.9900
11:8230504:CCTG:C	acceptor_loss	0.9900
11:8230505:C:CC	acceptor_gain	0.9900
11:8230505:C:T	acceptor_loss	0.9900
11:8230506:T:A	acceptor_loss	0.9900
11:8226600:T:C	acceptor_gain	0.9800
11:8226973:A:AC	donor_gain	0.9800
11:8226974:C:CC	donor_gain	0.9800
11:8227098:AGC:A	acceptor_gain	0.9800
11:8228187:G:C	donor_gain	0.9800
11:8230501:ACGC:A	acceptor_gain	0.9800

AlphaMissense

1042 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:8224673:A:C	C138W	1.000
11:8224674:C:G	C138S	1.000
11:8224674:C:T	C138Y	1.000
11:8224675:A:G	C138R	1.000
11:8224675:A:T	C138S	1.000
11:8224700:G:C	F129L	1.000
11:8224700:G:T	F129L	1.000
11:8224702:A:G	F129L	1.000
11:8224710:C:A	G126V	1.000
11:8224710:C:T	G126E	1.000
11:8224711:C:G	G126R	1.000
11:8224711:C:T	G126R	1.000
11:8224719:A:G	F123S	1.000
11:8226983:G:C	C119W	1.000
11:8226984:C:A	C119F	1.000
11:8226984:C:T	C119Y	1.000
11:8226985:A:G	C119R	1.000
11:8226992:G:C	C116W	1.000
11:8226993:C:T	C116Y	1.000
11:8226994:A:G	C116R	1.000
11:8226998:G:C	F114L	1.000
11:8226998:G:T	F114L	1.000
11:8226999:A:C	F114C	1.000
11:8226999:A:G	F114S	1.000
11:8227000:A:G	F114L	1.000
11:8227000:A:T	F114I	1.000
11:8227001:G:C	C113W	1.000
11:8227002:C:A	C113F	1.000
11:8227002:C:G	C113S	1.000
11:8227002:C:T	C113Y	1.000

dbSNP variants (sampled 300 via entrez): RS1000039567 (11:8241867 G>C), RS1000101161 (11:8246254 G>A), RS1000232443 (11:8236942 C>T), RS1000237108 (11:8252008 A>G), RS1000243900 (11:8237251 G>A,T), RS1000244484 (11:8264824 G>A), RS1000327424 (11:8267060 G>C), RS1000349420 (11:8239080 T>G), RS1000407349 (11:8225885 C>A,T), RS1000439662 (11:8249745 A>G), RS1000442433 (11:8231616 C>T), RS1000449244 (11:8267352 T>C,G), RS1000466851 (11:8243614 G>A,T), RS1000497466 (11:8242131 A>G), RS1000537138 (11:8234647 G>A,C)

Disease associations

OMIM: gene MIM:186921 | disease phenotypes: MIM:616792

GenCC curated gene-disease

Mondo (1): neuroblastoma, susceptibility to, 7 (MONDO:0014774)

Orphanet (1): Neuroblastoma (Orphanet:635)

HPO phenotypes

34 total (30 of 34 shown, HPO-id order):

HPO	Term
HP:0000520	Proptosis
HP:0000737	Irritability
HP:0000822	Hypertension
HP:0001017	Anemic pallor
HP:0001251	Ataxia
HP:0001336	Myoclonus
HP:0001482	Subcutaneous nodule
HP:0001824	Weight loss
HP:0001873	Thrombocytopenia
HP:0001892	Abnormal bleeding
HP:0001903	Anemia
HP:0001928	Abnormality of coagulation
HP:0001945	Fever
HP:0002028	Chronic diarrhea
HP:0002098	Respiratory distress
HP:0002176	Spinal cord compression
HP:0002277	Horner syndrome
HP:0002653	Bone pain
HP:0002716	Lymphadenopathy
HP:0002756	Pathologic fracture
HP:0003006	Neuroblastoma
HP:0003270	Abdominal distention
HP:0003281	Increased circulating ferritin concentration
HP:0003334	Elevated circulating catecholamine level
HP:0004375	Neoplasm of the nervous system
HP:0010543	Opsoclonus
HP:0011976	Elevated urinary catecholamine level
HP:0011977	Elevated urinary homovanillic acid
HP:0011978	Elevated urinary vanillylmandelic acid
HP:0012378	Fatigue

GWAS associations

21 associations (top):

Study	Trait	p-value
GCST000901_3	Neuroblastoma	5.000000e-16
GCST001527_10	Fasting blood glucose (BMI interaction)	2.000000e-07
GCST001660_3	Neuroblastoma	1.000000e-13
GCST002065_4	Alcohol consumption	7.000000e-07
GCST003485_7	Response to fenofibrate (HDL cholesterol levels)	2.000000e-06
GCST004510_5	Sporadic neuroblastoma	3.000000e-16
GCST004904_92	Body mass index	5.000000e-11
GCST005186_12	Fasting blood glucose	7.000000e-07
GCST005950_10	Body mass index x sex x age interaction (4df test)	6.000000e-11
GCST005951_51	Body mass index	8.000000e-11
GCST005953_4	Body mass index (age <50)	4.000000e-11
GCST006020_40	Diastolic blood pressure	7.000000e-07
GCST006021_36	Systolic blood pressure	2.000000e-06
GCST008363_80	Offspring birth weight	3.000000e-21
GCST008839_543	Height	2.000000e-08
GCST009701_4	Body mass index	8.000000e-06
GCST010725_20	Malaria	4.000000e-69
GCST010725_33	Malaria	2.000000e-67
GCST010725_51	Malaria	1.000000e-55
GCST011995_4	Restless legs syndrome	9.000000e-14
GCST012071_5	Response to selenium supplementation (change in plasma selenium concentration)	4.000000e-06

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004329	alcohol drinking
EFO:0007805	HDL cholesterol change measurement
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0006336	diastolic blood pressure
EFO:0006335	systolic blood pressure
EFO:0004344	birth weight
EFO:0005939	parental genotype effect measurement
EFO:0600021	response to dietary selenium supplementation

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
Valproic Acid	affects cotreatment, decreases expression, affects expression	5
Aflatoxin B1	increases methylation, increases expression	3
bisphenol F	affects cotreatment, increases methylation, decreases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
Benzo(a)pyrene	increases methylation, affects methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
trichostatin A	decreases expression	1
sulforaphane	decreases expression	1
sodium arsenite	increases expression	1
tri-o-cresyl phosphate	decreases expression	1
butylbenzyl phthalate	increases expression	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression, affects response to substance, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases reaction, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Carbamazepine	affects expression	1
Cisplatin	decreases expression, increases reaction	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment, decreases expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Rotenone	decreases expression	1

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_1667	RPMI-8402	Cancer cell line	Female
CVCL_A3X7	SEES3-1V human LMO1, clone1	Embryonic stem cell	Male
CVCL_A3X8	SEES3-1V human LMO1, clone2	Embryonic stem cell	Male
CVCL_A3X9	SEES3-1V human LMO1, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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