Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	221656
Gene name	Lysine demethylase 1B
Gene symbol	KDM1B
Synonyms (NCBI Gene)	AOF1C6orf193LSD2
Chromosome	6
Chromosome location	6p22.3
Summary	Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]

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Show/Hide all (161)

miRTarBase ID	miRNA	Experiments	Reference
MIRT019487	hsa-miR-148b-3p	Microarray	17612493
MIRT002552	hsa-miR-373-3p	Microarray	15685193
MIRT026955	hsa-miR-192-5p	Microarray	19074876
MIRT1083980	hsa-miR-1244	CLIP-seq
MIRT1083981	hsa-miR-1258	CLIP-seq
MIRT1083982	hsa-miR-1275	CLIP-seq
MIRT1083983	hsa-miR-129-5p	CLIP-seq
MIRT1083984	hsa-miR-1303	CLIP-seq
MIRT1083985	hsa-miR-1304	CLIP-seq
MIRT1083986	hsa-miR-148a	CLIP-seq
MIRT1083987	hsa-miR-148b	CLIP-seq
MIRT1083988	hsa-miR-152	CLIP-seq
MIRT1083989	hsa-miR-1908	CLIP-seq
MIRT1083990	hsa-miR-199a-3p	CLIP-seq
MIRT1083991	hsa-miR-199b-3p	CLIP-seq
MIRT1083992	hsa-miR-214	CLIP-seq
MIRT1083993	hsa-miR-302a	CLIP-seq
MIRT1083994	hsa-miR-302b	CLIP-seq
MIRT1083995	hsa-miR-302c	CLIP-seq
MIRT1083996	hsa-miR-302d	CLIP-seq
MIRT1083997	hsa-miR-302e	CLIP-seq
MIRT1083998	hsa-miR-3129-5p	CLIP-seq
MIRT1083999	hsa-miR-3140-3p	CLIP-seq
MIRT1084000	hsa-miR-3148	CLIP-seq
MIRT1084001	hsa-miR-3152-3p	CLIP-seq
MIRT1084002	hsa-miR-3180	CLIP-seq
MIRT1084003	hsa-miR-3180-3p	CLIP-seq
MIRT1084004	hsa-miR-3196	CLIP-seq
MIRT1084005	hsa-miR-331-5p	CLIP-seq
MIRT1084006	hsa-miR-338-5p	CLIP-seq
MIRT1084007	hsa-miR-33a	CLIP-seq
MIRT1084008	hsa-miR-33b	CLIP-seq
MIRT1084009	hsa-miR-3619-5p	CLIP-seq
MIRT1084010	hsa-miR-3650	CLIP-seq
MIRT1084011	hsa-miR-3668	CLIP-seq
MIRT1084012	hsa-miR-3688-3p	CLIP-seq
MIRT1084013	hsa-miR-372	CLIP-seq
MIRT1084014	hsa-miR-373	CLIP-seq
MIRT1084015	hsa-miR-4266	CLIP-seq
MIRT1084016	hsa-miR-4291	CLIP-seq
MIRT1084017	hsa-miR-4328	CLIP-seq
MIRT1084018	hsa-miR-4420	CLIP-seq
MIRT1084019	hsa-miR-4464	CLIP-seq
MIRT1084020	hsa-miR-4488	CLIP-seq
MIRT1084021	hsa-miR-4665-5p	CLIP-seq
MIRT1084022	hsa-miR-4678	CLIP-seq
MIRT1084023	hsa-miR-4695-5p	CLIP-seq
MIRT1084024	hsa-miR-4697-3p	CLIP-seq
MIRT1084025	hsa-miR-4697-5p	CLIP-seq
MIRT1084026	hsa-miR-4699-3p	CLIP-seq
MIRT1084027	hsa-miR-4703-3p	CLIP-seq
MIRT1084028	hsa-miR-4711-3p	CLIP-seq
MIRT1084029	hsa-miR-4748	CLIP-seq
MIRT1084030	hsa-miR-4767	CLIP-seq
MIRT1084031	hsa-miR-4779	CLIP-seq
MIRT1084032	hsa-miR-487a	CLIP-seq
MIRT1084033	hsa-miR-494	CLIP-seq
MIRT1084034	hsa-miR-499a-5p	CLIP-seq
MIRT1084035	hsa-miR-509-3p	CLIP-seq
MIRT1084036	hsa-miR-519a	CLIP-seq
MIRT1084037	hsa-miR-519b-3p	CLIP-seq
MIRT1084038	hsa-miR-519c-3p	CLIP-seq
MIRT1084039	hsa-miR-520a-3p	CLIP-seq
MIRT1084040	hsa-miR-520b	CLIP-seq
MIRT1084041	hsa-miR-520c-3p	CLIP-seq
MIRT1084042	hsa-miR-520d-3p	CLIP-seq
MIRT1084043	hsa-miR-520e	CLIP-seq
MIRT1084044	hsa-miR-520f	CLIP-seq
MIRT1084045	hsa-miR-544b	CLIP-seq
MIRT1084046	hsa-miR-663	CLIP-seq
MIRT1084047	hsa-miR-761	CLIP-seq
MIRT1084048	hsa-miR-922	CLIP-seq
MIRT1083980	hsa-miR-1244	CLIP-seq
MIRT1083990	hsa-miR-199a-3p	CLIP-seq
MIRT1083991	hsa-miR-199b-3p	CLIP-seq
MIRT1083992	hsa-miR-214	CLIP-seq
MIRT1083998	hsa-miR-3129-5p	CLIP-seq
MIRT2021261	hsa-miR-3143	CLIP-seq
MIRT1084000	hsa-miR-3148	CLIP-seq
MIRT1084009	hsa-miR-3619-5p	CLIP-seq
MIRT2021262	hsa-miR-3679-3p	CLIP-seq
MIRT1084012	hsa-miR-3688-3p	CLIP-seq
MIRT1084016	hsa-miR-4291	CLIP-seq
MIRT1084018	hsa-miR-4420	CLIP-seq
MIRT2021263	hsa-miR-4422	CLIP-seq
MIRT2021264	hsa-miR-4446-5p	CLIP-seq
MIRT1084019	hsa-miR-4464	CLIP-seq
MIRT1084027	hsa-miR-4703-3p	CLIP-seq
MIRT1084029	hsa-miR-4748	CLIP-seq
MIRT1084034	hsa-miR-499a-5p	CLIP-seq
MIRT2021265	hsa-miR-513a-3p	CLIP-seq
MIRT1084045	hsa-miR-544b	CLIP-seq
MIRT2021266	hsa-miR-607	CLIP-seq
MIRT1084047	hsa-miR-761	CLIP-seq
MIRT1084048	hsa-miR-922	CLIP-seq
MIRT2252792	hsa-miR-1279	CLIP-seq
MIRT2252793	hsa-miR-186	CLIP-seq
MIRT2252794	hsa-miR-2113	CLIP-seq
MIRT2252795	hsa-miR-218	CLIP-seq
MIRT1083993	hsa-miR-302a	CLIP-seq
MIRT1083994	hsa-miR-302b	CLIP-seq
MIRT1083995	hsa-miR-302c	CLIP-seq
MIRT1083996	hsa-miR-302d	CLIP-seq
MIRT1083997	hsa-miR-302e	CLIP-seq
MIRT2252796	hsa-miR-3133	CLIP-seq
MIRT1084000	hsa-miR-3148	CLIP-seq
MIRT1084007	hsa-miR-33a	CLIP-seq
MIRT1084008	hsa-miR-33b	CLIP-seq
MIRT2252797	hsa-miR-34c-3p	CLIP-seq
MIRT2252798	hsa-miR-3607-3p	CLIP-seq
MIRT2252799	hsa-miR-3616-5p	CLIP-seq
MIRT2252800	hsa-miR-3647-5p	CLIP-seq
MIRT1084012	hsa-miR-3688-3p	CLIP-seq
MIRT1084013	hsa-miR-372	CLIP-seq
MIRT1084014	hsa-miR-373	CLIP-seq
MIRT2252801	hsa-miR-4643	CLIP-seq
MIRT2252802	hsa-miR-4653-3p	CLIP-seq
MIRT2252803	hsa-miR-4693-5p	CLIP-seq
MIRT2252804	hsa-miR-4729	CLIP-seq
MIRT2252805	hsa-miR-4753-3p	CLIP-seq
MIRT2252806	hsa-miR-505	CLIP-seq
MIRT1084036	hsa-miR-519a	CLIP-seq
MIRT1084037	hsa-miR-519b-3p	CLIP-seq
MIRT1084038	hsa-miR-519c-3p	CLIP-seq
MIRT1084039	hsa-miR-520a-3p	CLIP-seq
MIRT1084040	hsa-miR-520b	CLIP-seq
MIRT1084041	hsa-miR-520c-3p	CLIP-seq
MIRT1084042	hsa-miR-520d-3p	CLIP-seq
MIRT1084043	hsa-miR-520e	CLIP-seq
MIRT1084044	hsa-miR-520f	CLIP-seq
MIRT2252807	hsa-miR-573	CLIP-seq
MIRT2252808	hsa-miR-626	CLIP-seq
MIRT2438112	hsa-miR-192	CLIP-seq
MIRT2438113	hsa-miR-215	CLIP-seq
MIRT2021265	hsa-miR-513a-3p	CLIP-seq
MIRT1083980	hsa-miR-1244	CLIP-seq
MIRT1083990	hsa-miR-199a-3p	CLIP-seq
MIRT1083991	hsa-miR-199b-3p	CLIP-seq
MIRT1083992	hsa-miR-214	CLIP-seq
MIRT1083998	hsa-miR-3129-5p	CLIP-seq
MIRT1084009	hsa-miR-3619-5p	CLIP-seq
MIRT1084016	hsa-miR-4291	CLIP-seq
MIRT1084027	hsa-miR-4703-3p	CLIP-seq
MIRT1084034	hsa-miR-499a-5p	CLIP-seq
MIRT2452318	hsa-miR-548a-5p	CLIP-seq
MIRT2452319	hsa-miR-548ab	CLIP-seq
MIRT2452320	hsa-miR-548ak	CLIP-seq
MIRT2452321	hsa-miR-548b-5p	CLIP-seq
MIRT2452322	hsa-miR-548c-5p	CLIP-seq
MIRT2452323	hsa-miR-548d-5p	CLIP-seq
MIRT2452324	hsa-miR-548h	CLIP-seq
MIRT2452325	hsa-miR-548i	CLIP-seq
MIRT2452326	hsa-miR-548j	CLIP-seq
MIRT2452327	hsa-miR-548n	CLIP-seq
MIRT2452328	hsa-miR-548t	CLIP-seq
MIRT2452329	hsa-miR-548w	CLIP-seq
MIRT2452330	hsa-miR-548y	CLIP-seq
MIRT2452331	hsa-miR-559	CLIP-seq
MIRT2452332	hsa-miR-577	CLIP-seq
MIRT1084047	hsa-miR-761	CLIP-seq
MIRT1084048	hsa-miR-922	CLIP-seq

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IDA	30970244
GO:0000786	Component	Nucleosome	IDA	23260659
GO:0005515	Function	Protein binding	IPI	23260659, 28514442, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS	19727073
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0008270	Function	Zinc ion binding	IDA	23260659, 23266887
GO:0008270	Function	Zinc ion binding	IEA
GO:0016491	Function	Oxidoreductase activity	IBA
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0032452	Function	Histone demethylase activity	TAS
GO:0032453	Function	Histone H3K4 demethylase activity	IEA
GO:0040029	Process	Epigenetic regulation of gene expression	IEA
GO:0042393	Function	Histone binding	IDA	23260659
GO:0044726	Process	Epigenetic programing of female pronucleus	IEA
GO:0045815	Process	Transcription initiation-coupled chromatin remodeling	IDA	30970244
GO:0046872	Function	Metal ion binding	IEA
GO:0050660	Function	Flavin adenine dinucleotide binding	IEA
GO:0071514	Process	Genomic imprinting	IEA
GO:0071514	Process	Genomic imprinting	ISS	19727073
GO:0071949	Function	FAD binding	IDA	23260659, 23266887
GO:0140682	Function	FAD-dependent H3K4me/H3K4me3 demethylase activity	IDA	23260659, 23266887, 23357850, 30970244
GO:0140682	Function	FAD-dependent H3K4me/H3K4me3 demethylase activity	IEA

MIM	HGNC	e!Ensembl
613081	21577	ENSG00000165097

Q8NB78

Protein name

Lysine-specific histone demethylase 2 (EC 1.14.99.66) (Flavin-containing amine oxidase domain-containing protein 1) (Lysine-specific histone demethylase 1B)

Protein function

Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by

PDB

4FWE , 4FWF , 4FWJ , 4GU0 , 4GU1 , 4GUR , 4GUS , 4GUT , 4GUU , 4HSU , 6R1U , 6R25 , 7XE1 , 7XE2 , 7XE3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF07496	zf-CW	138 → 191	CW-type Zinc Finger	Domain
PF04433	SWIRM	282 → 364	SWIRM domain	Domain
PF01593	Amino_oxidase	392 → 820	Flavin containing amine oxidoreductase	Domain

Sequence

MATPRGRTKKKASFDHSPDSLPLRSSGRQAKKKATETTDEDEDGGSEKKYRKCEKAGCTA
TCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSN
GKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPE
TSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRA
AATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEY
SRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKG
LINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGR
VWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTID
KRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHL
SNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQC
IDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIE
KIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVAS
VRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYD
IIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

Sequence length

822

Interactions

View interactions

	Reactome
			HDMs demethylate histones UCH proteinases NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FIBRILLATION	—	CTD, Disgenet, GWAS catalog CTD, Disgenet, GWAS catalog CTD, Disgenet, GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATRIAL FLUTTER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (25)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Alzheimer`s Disease	Alzheimer disease	GWASCAT_DG	26830138		★★★★★ ★☆☆☆☆ Found in Text Mining only
Atrial Fibrillation	Atrial Fibrillation	GWASCAT_DG	29892015, 30061737		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Atrial Fibrillation	Atrial Fibrillation	CTD_human_DG	29892015		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	24924415, 29137219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	36002648	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	31160694	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	32726297	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	31160694		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ewings sarcoma	Ewing sarcoma	BEFREE	31231465		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	26766590		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	26766590		★★★★★ ★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	32994395	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	24924415, 29137219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	30846414		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	30944080		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	25036127, 29137219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	29137219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	25036127, 29137219		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	31108893	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	30846414		★★★★★ ★☆☆☆☆ Found in Text Mining only
Paroxysmal atrial fibrillation	Paroxysmal atrial fibrillation	CTD_human_DG	29892015		★★★★★ ★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	31160694		★★★★★ ★☆☆☆☆ Found in Text Mining only
Small Cell Lung Carcinoma	Small cell lung carcinoma	Pubtator	29845195	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	22847005	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	30944080		★★★★★ ★☆☆☆☆ Found in Text Mining only

KDM1B (lysine demethylase 1B)