H1-3

Summary

H1-3 (H1.3 linker histone, cluster member, HGNC:4717) is a protein-coding gene on chromosome 6p22.2, encoding Histone H1.3 (P16402). Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber.

Histones are basic nuclear proteins responsible for nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H1 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6.

Source: NCBI Gene 3007 — RefSeq curated summary.

At a glance

• GWAS associations: 16
• Clinical variants (ClinVar): 119 total
• Druggable target: yes
• MANE Select transcript: NM_005320

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4717
Approved symbol	H1-3
Name	H1.3 linker histone, cluster member
Location	6p22.2
Locus type	gene with protein product
Status	Approved
Aliases	H1.3, H1d, H1s-2
Ensembl gene	ENSG00000124575
Ensembl biotype	protein_coding
OMIM	142210
Entrez	3007

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000244534

RefSeq mRNA: 1 — MANE Select: NM_005320 NM_005320

CCDS: CCDS4597

Canonical transcript exons

ENST00000244534 — 1 exons

Exon	Start	End
ENSE00001989449	26234212	26234987

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 96.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 254.4563 / max 3154.6240, expressed in 1711 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72336	254.4563	1711

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	96.32	gold quality
calcaneal tendon	UBERON:0003701	94.33	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.37	gold quality
colonic epithelium	UBERON:0000397	88.83	gold quality
tendon	UBERON:0000043	87.89	gold quality
bone marrow cell	CL:0002092	85.82	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.91	gold quality
tendon of biceps brachii	UBERON:0008188	78.99	gold quality
bone marrow	UBERON:0002371	75.64	gold quality
ventricular zone	UBERON:0003053	73.01	gold quality
tonsil	UBERON:0002372	69.72	gold quality
embryo	UBERON:0000922	67.89	gold quality
sural nerve	UBERON:0015488	67.69	gold quality
ganglionic eminence	UBERON:0004023	67.42	gold quality
blood	UBERON:0000178	63.50	gold quality
mucosa of transverse colon	UBERON:0004991	63.05	gold quality
amniotic fluid	UBERON:0000173	63.02	gold quality
thymus	UBERON:0002370	61.02	silver quality
corpus callosum	UBERON:0002336	60.86	gold quality
heart right ventricle	UBERON:0002080	60.59	gold quality
lymph node	UBERON:0000029	60.33	gold quality
granulocyte	CL:0000094	58.88	gold quality
monocyte	CL:0000576	57.61	gold quality
mononuclear cell	CL:0000842	57.54	gold quality
gluteal muscle	UBERON:0002000	57.51	gold quality
triceps brachii	UBERON:0001509	57.36	gold quality
vagina	UBERON:0000996	57.28	gold quality
leukocyte	CL:0000738	56.70	gold quality
rectum	UBERON:0001052	56.68	gold quality
uterine cervix	UBERON:0000002	55.06	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-HCAD-56	yes	2996.53
E-MTAB-7407	yes	780.27
E-MTAB-8894	yes	563.21
E-MTAB-11121	yes	345.34
E-MTAB-8271	yes	289.22
E-MTAB-9467	yes	31.31
E-CURD-122	yes	22.33
E-ANND-3	yes	8.85
E-MTAB-6911	no	182.98
E-MTAB-6108	no	165.51

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 7)

• confirmed N-terminal acetylation on all isoforms plus a single internal acetylation site; phosphorylation sites were located on peptides containing the cyclin dependent kinase (CDK) consensus motif (PMID:15595731)
• overexpression of histone cluster 1 is associated with recurrence in meningiomas. (PMID:20685720)
• Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma. (PMID:24435047)
• Integration with apoptotic intermediates (via C-terminal tail interactions) may constitute a more generalized function of linker histone isoforms in apoptotic cascades. (PMID:24525734)
• Histone H1 organizes and maintains an extensive protein-protein interaction network in the nucleolus required for nucleolar structure and integrity. (PMID:25584861)
• Results show that histone H1.3, was identified only in non-neoplastic MCF-10A breast cells but not in metastatic MDA-MB-231 breast cancer cells . (PMID:26209608)
• Data suggest that NPM1mut AML prognosis depends on the epigenetic silencing of the HIST1 cluster and that, among the H3K27me3 silenced histone genes, HIST1H1D plays a role in AML blast differentiation. (PMID:31606046)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	h1l1	ENSDARG00000074012
danio_rerio	si:dkey-23a13.9	ENSDARG00000105431
mus_musculus	H1f3	ENSMUSG00000052565
rattus_norvegicus	H4f3	ENSRNOG00000090923
caenorhabditis_elegans		WBGENE00001853
caenorhabditis_elegans		WBGENE00001854
caenorhabditis_elegans		WBGENE00001855
caenorhabditis_elegans	hil-5	WBGENE00001856
caenorhabditis_elegans		WBGENE00001857

Paralogs (9): H1-1 (ENSG00000124610), H1-4 (ENSG00000168298), H1-8 (ENSG00000178804), H1-5 (ENSG00000184357), H1-10 (ENSG00000184897), H1-7 (ENSG00000187166), H1-6 (ENSG00000187475), H1-2 (ENSG00000187837), H1-0 (ENSG00000189060)

Protein

Protein identifiers

Histone H1.3 — P16402 (reviewed: P16402)

Alternative names: Histone H1c, Histone H1s-2

All UniProt accessions (1): P16402

UniProt curated annotations — full annotation on UniProt →

Function. Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers and promote formation of the H3K27me3 mark by the PRC2/EED-EZH2 complex. Together with histone H1-3, histone H1-3 acts as a regulator of splicing, most specifically exon skipping and intron retention events: histone H1-3 has a high affinity for introns and regulates splicing by affecting RNA polymerase II (RNAPII) elongation. Also acts as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation.

Subunit / interactions. Associates with nucleosomes, promoting condensation into higher-order structured chromatin.

Subcellular location. Nucleus. Chromosome.

Post-translational modifications. Deamidation of Asn-77 and Asn-78 by CTPS1 in response to DNA damage promotes subsequent acetylation of histone H1 at Lys-76 (H1K75ac). Acetylated at Lys-76 (H1K75ac) by EP300 following deamidation of Asn-77 and Asn-78 by CTPS1 in response to DNA damage, thereby increasing chromatin accessibility to facilitate the recruitment of DNA repair proteins. H1 histones are progressively phosphorylated during the cell cycle, becoming maximally phosphorylated during late G2 phase and M phase, and being dephosphorylated sharply thereafter. Citrullination at Arg-55 (H1R54ci) by PADI4 takes place within the DNA-binding site of H1 and results in its displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance.

Domain organisation. The C-terminal domain is required for high-affinity binding to chromatin.

Induction. Expression is activated by transcription factor CRAMP1, in collaboration with NPAT and GON4L.

Similarity. Belongs to the histone H1/H5 family.

RefSeq proteins (1): NP_005311* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005818	Histone_H1/H5_H15	Domain
IPR005819	H1/H5	Family
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily

Pfam: PF00538

UniProt features (52 total): modified residue 32, compositionally biased region 7, strand 4, helix 3, region of interest 2, initiator methionine 1, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7XX5	X-RAY DIFFRACTION	3.19

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P16402-F1	64.03	0.29

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 (32): 2, 2, 17, 18, 26, 35, 35, 47, 47, 53, 53, 55, 64, 65, 65, 76, 76, 77, 78, 86 …

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-140342	Apoptosis induced DNA fragmentation
R-HSA-2559584	Formation of Senescence-Associated Heterochromatin Foci (SAHF)

MSigDB gene sets: 132 (showing top): GOBP_CHROMOSOME_ORGANIZATION, REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION, E2F_Q4_01, GOBP_REGULATION_OF_DNA_RECOMBINATION, ENK_UV_RESPONSE_KERATINOCYTE_UP, GOBP_NEGATIVE_REGULATION_OF_DNA_RECOMBINATION, GOBP_CHROMOSOME_CONDENSATION, E2F_Q3, GOBP_RNA_SPLICING, MODULE_284, GOBP_REGULATION_OF_MRNA_SPLICING_VIA_SPLICEOSOME, E2F1_Q3, FISCHER_DREAM_TARGETS, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, REACTOME_APOPTOSIS

GO Biological Process (7): negative regulation of transcription by RNA polymerase II (GO:0000122), nucleosome assembly (GO:0006334), chromosome condensation (GO:0030261), negative regulation of DNA recombination (GO:0045910), regulation of mRNA splicing, via spliceosome (GO:0048024), chromatin organization (GO:0006325), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (7): double-stranded DNA binding (GO:0003690), RNA binding (GO:0003723), structural constituent of chromatin (GO:0030527), chromatin DNA binding (GO:0031490), nucleosomal DNA binding (GO:0031492), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (6): chromatin (GO:0000785), nucleosome (GO:0000786), euchromatin (GO:0000791), heterochromatin (GO:0000792), nucleus (GO:0005634), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Apoptotic execution phase	1
DNA Damage/Telomere Stress Induced Senescence	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chromatin	4
transcription by RNA polymerase II	2
DNA binding	2
nucleic acid binding	2
regulation of transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
chromatin organization	1
nucleosome organization	1
protein-DNA complex assembly	1
chromosome organization	1
regulation of DNA recombination	1
DNA recombination	1
negative regulation of DNA metabolic process	1
mRNA splicing, via spliceosome	1
regulation of RNA splicing	1
regulation of mRNA processing	1
cellular component organization	1
regulation of DNA-templated transcription	1
structural molecule activity	1
chromatin binding	1
chromatin DNA binding	1
nucleosome binding	1
binding	1
chromosome	1
cellular anatomical structure	1
protein-DNA complex	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

900 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
H1-3	H2AC20	Q16777	772
H1-3	H2AC19	P20670	771
H1-3	H1-7	Q75WM6	762
H1-3	H2BC21	Q16778	751
H1-3	H1-8	Q8IZA3	749
H1-3	H1-2	P16403	622
H1-3	H1-4	P10412	594
H1-3	DNMT3B	Q9UBC3	497
H1-3	DNMT1	P26358	490
H1-3	ANXA6	P08133	473
H1-3	H2BC9	Q93079	468
H1-3	NUCLEOLIN	P19338	455
H1-3	PSME3IP1	Q9GZU8	449
H1-3	H3C1	P02295	438
H1-3	DFFB	O76075	432

IntAct

102 interactions, top by confidence:

A	B	Type	Score
N	HNRNPR	psi-mi:“MI:0914”(association)	0.730
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
ZNF662	H1-3	psi-mi:“MI:0915”(physical association)	0.590
CCNB1IP1	H1-3	psi-mi:“MI:0915”(physical association)	0.590
H1-3	HMGA1	psi-mi:“MI:0915”(physical association)	0.560
Zfp36	CNOT1	psi-mi:“MI:0914”(association)	0.560
YWHAZ	LMNA	psi-mi:“MI:0914”(association)	0.560
HOXB5	VPS37C	psi-mi:“MI:0914”(association)	0.530
USP38	AHSG	psi-mi:“MI:0914”(association)	0.530
MOK	H1-3	psi-mi:“MI:0914”(association)	0.530
ZC3HAV1	KHNYN	psi-mi:“MI:0914”(association)	0.530
PSG3	MGRN1	psi-mi:“MI:0914”(association)	0.530
EBNA-LP	HAX1	psi-mi:“MI:0914”(association)	0.530
PDE6H	H1-3	psi-mi:“MI:0915”(physical association)	0.400
H1-3	H1-5	psi-mi:“MI:0915”(physical association)	0.400
H1-3	H1-4	psi-mi:“MI:0915”(physical association)	0.400
H1-3	H1-2	psi-mi:“MI:0915”(physical association)	0.400
H1-3	H3C13	psi-mi:“MI:0915”(physical association)	0.400
H1-3	H1-1	psi-mi:“MI:0915”(physical association)	0.400
AGPAT2	H1-3	psi-mi:“MI:0915”(physical association)	0.400
	GNAT3	psi-mi:“MI:0915”(physical association)	0.400
MYO1B	H1-3	psi-mi:“MI:0915”(physical association)	0.400
FRMD6	H1-3	psi-mi:“MI:0915”(physical association)	0.400
IVD	H1-3	psi-mi:“MI:0915”(physical association)	0.400
MAPT	C11orf98	psi-mi:“MI:0914”(association)	0.350

BioGRID (430): HIST1H1D (Biochemical Activity), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS), HIST1H1D (Affinity Capture-MS)

ESM2 similar proteins: A7MAZ5, D3ZBN0, D4A3K5, G3N131, P02251, P02252, P02253, P02254, P06350, P06893, P07305, P08284, P08285, P08286, P08287, P08288, P09426, P09987, P10412, P15796, P15864, P15865, P15866, P15867, P15870, P16401, P16402, P16403, P21895, P22844, P22845, P23444, P27806, P35060, P40262, P40263, P40264, P40265, P40266, P40275

Diamond homologs: A7MAZ5, D3ZBN0, D3ZZW6, D4A3K5, G3N131, O01833, O16277, P02251, P02252, P02253, P02254, P02255, P02256, P02257, P02258, P02259, P06144, P06348, P06349, P06350, P06513, P06892, P06893, P06894, P07305, P07796, P08284, P08285, P08286, P08287, P08288, P09426, P09987, P10412, P10922, P15796, P15864, P15865, P15866, P15867

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 133 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of Senescence-Associated Heterochromatin Foci (SAHF)	7	51.1×	2e-08
Dengue Virus Genome Translation and Replication	5	17.2×	1e-03
AUF1 (hnRNP D0) binds and destabilizes mRNA	5	13.5×	4e-03
Programmed Cell Death	6	9.6×	4e-03
mRNA Polyadenylation	8	7.6×	1e-03
Dengue Virus-Host Interactions	12	6.0×	2e-04
mRNA Splicing - Major Pathway	9	5.3×	4e-03

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of DNA recombination	5	46.0×	5e-05
chromosome condensation	5	34.5×	9e-05
nucleosome assembly	9	10.4×	9e-05
negative regulation of translation	6	9.6×	6e-03
endocytosis	8	6.2×	6e-03

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	109
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

114 predictions. Top by Δscore:

Variant	Effect	Δscore
6:26234270:A:AC	donor_gain	0.6500
6:26234271:C:CC	donor_gain	0.6500
6:26234459:CCTT:C	donor_gain	0.6400
6:26234454:CTTTA:C	donor_loss	0.6200
6:26234455:TTTA:T	donor_loss	0.6200
6:26234456:TTA:T	donor_loss	0.6200
6:26234457:TACC:T	donor_loss	0.6200
6:26234459:C:A	donor_loss	0.6200
6:26234460:C:G	donor_loss	0.5900
6:26234300:TTGTA:T	donor_gain	0.5700
6:26234669:CCAAG:C	donor_gain	0.5600
6:26234543:T:TA	donor_gain	0.5200
6:26234362:G:C	donor_gain	0.4900
6:26234507:C:CT	donor_gain	0.4800
6:26234508:C:CT	donor_gain	0.4600
6:26234296:G:A	donor_gain	0.4400
6:26234316:C:A	donor_gain	0.4400
6:26234325:A:AC	donor_gain	0.4400
6:26234652:CAGAG:C	donor_gain	0.4400
6:26234655:A:AC	donor_gain	0.4400
6:26234661:TTTGC:T	donor_loss	0.4400
6:26234662:TTGCT:T	donor_loss	0.4400
6:26234663:TGCT:T	donor_loss	0.4400
6:26234664:GCT:G	donor_loss	0.4400
6:26234665:C:T	donor_loss	0.4400
6:26234666:T:TG	donor_loss	0.4400
6:26234667:CA:C	donor_loss	0.4400
6:26234668:ACCA:A	donor_loss	0.4400
6:26234669:CCAA:C	donor_loss	0.4400
6:26234651:CCAGA:C	donor_gain	0.4300

AlphaMissense

1413 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:26234616:G:C	F106L	1.000
6:26234616:G:T	F106L	1.000
6:26234617:A:G	F106S	1.000
6:26234618:A:G	F106L	1.000
6:26234617:A:C	F106C	0.999
6:26234623:C:T	G104D	0.999
6:26234632:C:T	G101D	0.999
6:26234638:C:T	G99D	0.999
6:26234639:C:A	G99C	0.999
6:26234639:C:G	G99R	0.999
6:26234653:A:T	L94Q	0.999
6:26234680:A:T	L85H	0.999
6:26234742:C:A	K64N	0.999
6:26234742:C:G	K64N	0.999
6:26234764:C:T	G57D	0.999
6:26234765:C:G	G57R	0.999
6:26234623:C:A	G104V	0.998
6:26234624:C:A	G104C	0.998
6:26234624:C:G	G104R	0.998
6:26234629:G:T	A102D	0.998
6:26234638:C:A	G99V	0.998
6:26234639:C:T	G99S	0.998
6:26234692:A:C	I81S	0.998
6:26234692:A:G	I81T	0.998
6:26234695:C:G	R80P	0.998
6:26234696:G:T	R80S	0.998
6:26234734:A:T	L67H	0.998
6:26234746:A:T	L63H	0.998
6:26234800:A:C	I45S	0.998
6:26234800:A:T	I45N	0.998

dbSNP variants (sampled 300 via entrez): RS1000001786 (6:26234203 T>A,C), RS1000688486 (6:26234106 C>A,T), RS1000795773 (6:26234709 T>C,G), RS1001326976 (6:26234124 A>G), RS1001559225 (6:26234994 T>A,C,G), RS1002001753 (6:26235244 A>G), RS1002565132 (6:26234105 A>G), RS1003004962 (6:26236576 C>T), RS1003180995 (6:26233987 A>C,G,T), RS1003233288 (6:26236187 T>C), RS1003288000 (6:26236175 T>A), RS1004369486 (6:26235902 ATT>A,AT,ATTT), RS1004423517 (6:26236143 C>T), RS1005064947 (6:26236091 A>G), RS1005861220 (6:26233894 C>G)

Disease associations

OMIM: gene MIM:142210 | 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
GCST000176_8	Height	4.000000e-17
GCST000372_10	Height	6.000000e-12
GCST004521_113	Autism spectrum disorder or schizophrenia	3.000000e-19
GCST004521_142	Autism spectrum disorder or schizophrenia	2.000000e-09
GCST004521_169	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_69	Autism spectrum disorder or schizophrenia	8.000000e-24
GCST004521_83	Autism spectrum disorder or schizophrenia	1.000000e-13
GCST006100_2	Strenuous sports or other exercises	1.000000e-09
GCST007294_143	Body fat distribution (trunk fat ratio)	5.000000e-29
GCST007294_82	Body fat distribution (trunk fat ratio)	1.000000e-48
GCST007295_120	Body fat distribution (leg fat ratio)	2.000000e-46
GCST007295_91	Body fat distribution (leg fat ratio)	1.000000e-26
GCST010141_1	Beef consumption	7.000000e-13
GCST010143_19	Meat-related diet	5.000000e-13
GCST010143_31	Meat-related diet	7.000000e-09
GCST010143_5	Meat-related diet	4.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008002	physical activity measurement
EFO:0004341	body fat distribution
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066306 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance	3
Air Pollutants	affects cotreatment, increases abundance, increases expression, decreases expression	3
Particulate Matter	decreases expression, increases abundance, increases expression	3
bisphenol A	decreases expression	2
trichostatin A	decreases expression	2
perfluorooctanoic acid	decreases expression, increases expression	2
potassium chromate(VI)	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	decreases expression	2
afuresertib	decreases expression	1
FR900359	decreases phosphorylation	1
geldanamycin	increases expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
arsenite	increases reaction, affects binding	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
ochratoxin A	decreases expression, affects cotreatment	1
versicolorin A	decreases expression	1
hydroquinone	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
mercuric bromide	decreases expression	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
picene	increases expression	1
tamibarotene	affects expression	1
chromium hexavalent ion	decreases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
monomethylarsonous acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652910	Binding	Binding affinity to human HIST1H1D incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

14 cell lines: 14 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_C9JY	WAe001-A-89	Embryonic stem cell	Male
CVCL_C9JZ	WAe001-A-90	Embryonic stem cell	Male
CVCL_C9KA	WAe001-A-C	Embryonic stem cell	Male
CVCL_C9KB	WAe001-A-D	Embryonic stem cell	Male
CVCL_C9KK	WAe001-A-M	Embryonic stem cell	Male
CVCL_C9KL	WAe001-A-N	Embryonic stem cell	Male
CVCL_C9KX	WAe001-A-Y	Embryonic stem cell	Male
CVCL_C9KY	WAe001-A-Z	Embryonic stem cell	Male
CVCL_C9L3	WAe001-A-1E	Embryonic stem cell	Male
CVCL_C9L4	WAe001-A-1F	Embryonic stem cell	Male

Clinical trials (associated diseases)

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