KDM6B
lysine demethylase 6B | KIAA0346, JMJD3

The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]

Member of: DE-4 DE-4.29 Developmental clusters: GC6
Biological processes 32 terms
MLL3/4 complex (GO:0044666)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)beta-catenin binding (GO:0008013)cardiac muscle cell differentiation (GO:0055007)cardiac muscle cell differentiation (GO:0055007)chromatin DNA binding (GO:0031490)chromatin binding (GO:0003682)chromatin remodeling (GO:0006338)chromatin remodeling (GO:0006338)endothelial cell differentiation (GO:0045446)endothelial cell differentiation (GO:0045446)heart development (GO:0007507)hippocampus development (GO:0021766)histone H3K27me2/H3K27me3 demethylase activity (GO:0071558)histone H3K27me2/H3K27me3 demethylase activity (GO:0071558)histone H3K27me2/H3K27me3 demethylase activity (GO:0071558)histone demethylase activity (GO:0032452)inflammatory response to antigenic stimulus (GO:0002437)mesodermal cell differentiation (GO:0048333)mesodermal cell differentiation (GO:0048333)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of cold-induced thermogenesis (GO:0120162)positive regulation of cold-induced thermogenesis (GO:0120162)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of gene expression (GO:0010468)response to activity (GO:0014823)response to fungicide (GO:0060992)sequence-specific DNA binding (GO:0043565)
Expression (TPM)
KDM6B — as a Regulated Gene

TFs regulating KDM6B 0 TFs

Transcription factors with Perturb-seq knockdown data for KDM6B. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = KDM6B upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to KDM6B

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of KDM6B, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr17:7,548,693–7,549,285 295.9 kb Distal (>10kb) Multiome 387
chr17:7,560,249–7,562,536 283.0 kb Distal (>10kb) Multiome 759
chr17:7,572,039–7,574,418 271.0 kb Distal (>10kb) Multiome 1071
chr17:7,583,063–7,584,547 261.1 kb Distal (>10kb) Multiome 921
chr17:7,588,871–7,590,534 254.8 kb Distal (>10kb) Multiome 319
chr17:7,614,065–7,615,780 229.8 kb Distal (>10kb) Multiome 708
chr17:7,627,090–7,628,247 217.1 kb Distal (>10kb) Multiome 712
chr17:7,650,010–7,652,127 194.1 kb Distal (>10kb) Multiome 467
chr17:7,685,876–7,686,907 158.6 kb Distal (>10kb) Multiome 765
chr17:7,687,867–7,688,863 156.6 kb Distal (>10kb) Multiome 700
chr17:7,703,383–7,703,975 141.3 kb Distal (>10kb) Multiome 141
chr17:7,704,799–7,705,590 139.8 kb Distal (>10kb) Multiome 325
chr17:7,716,832–7,717,983 127.6 kb Distal (>10kb) Multiome 759
chr17:7,833,417–7,837,960 9.3 kb Proximal (<10kb) Multiome 1160
chr17:7,841,438–7,843,228 2.7 kb Proximal (<10kb) Multiome 861
chr17:7,843,355–7,844,130 9.1 kb Proximal (<10kb) 614
chr17:7,844,349–7,845,186 3 bp At TSS Multiome 617
chr17:7,851,538–7,852,239 6.9 kb Proximal (<10kb) Multiome 531
chr17:7,853,062–7,853,638 8.1 kb Proximal (<10kb) 99
chr17:7,854,798–7,855,188 9.9 kb Proximal (<10kb) 106
chr17:7,856,600–7,858,747 12.6 kb Distal (>10kb) Multiome 942
chr17:7,885,205–7,885,734 40.4 kb Distal (>10kb) Multiome 371
chr17:7,887,616–7,888,198 42.9 kb Distal (>10kb) Multiome 581
chr17:7,915,430–7,916,499 71.0 kb Distal (>10kb) Multiome 869
chr17:7,922,863–7,923,421 78.1 kb Distal (>10kb) Multiome 205
chr17:7,929,559–7,930,172 84.9 kb Distal (>10kb) Multiome 106
chr17:7,931,533–7,932,876 87.2 kb Distal (>10kb) Multiome 767
chr17:7,971,685–7,972,375 127.0 kb Distal (>10kb) Multiome 45
chr17:7,989,908–7,990,676 145.4 kb Distal (>10kb) Multiome 652
chr17:8,015,966–8,016,968 171.1 kb Distal (>10kb) Multiome 339
chr17:8,068,609–8,069,844 223.9 kb Distal (>10kb) Multiome 100
chr17:8,079,261–8,080,640 234.6 kb Distal (>10kb) Multiome 613
chr17:8,109,567–8,110,530 265.4 kb Distal (>10kb) Multiome 360
chr17:8,117,780–8,119,396 274.0 kb Distal (>10kb) Multiome 684
chr17:8,119,590–8,122,560 275.7 kb Distal (>10kb) Multiome 968
chr17:8,125,308–8,126,995 280.8 kb Distal (>10kb) Multiome 724
chr17:8,138,425–8,139,804 294.1 kb Distal (>10kb) Multiome 981

Genome Browser

Genomic view of the KDM6B locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr17:7,538,693 – 8,149,804
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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