ZNF490

zinc finger protein 490 | KIAA1198

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Member of: DE-10 DE-10.4

Biological processes 7 terms

DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)regulation of DNA-templated transcription (GO:0006355)regulation of transcription by RNA polymerase II (GO:0006357)

Expression (TPM)

TFs regulating ZNF490 0 TFs

Transcription factors with Perturb-seq knockdown data for ZNF490. 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 = ZNF490 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to ZNF490

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ZNF490, 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.

Element	Dist. to TSS	Link type	TFs
chr19:12,365,585–12,366,054	245.1 kb	Distal (>10kb) Multiome	577
chr19:12,400,090–12,401,657	209.6 kb	Distal (>10kb) Multiome	671
chr19:12,440,217–12,441,483	169.7 kb	Distal (>10kb) Multiome	565
chr19:12,484,131–12,485,387	126.0 kb	Distal (>10kb) Multiome	664
chr19:12,495,009–12,495,882	115.4 kb	Distal (>10kb) Multiome	824
chr19:12,550,951–12,551,971	59.3 kb	Distal (>10kb) Multiome	976
chr19:12,571,455–12,571,942	39.1 kb	Distal (>10kb) Multiome	36
chr19:12,610,516–12,611,613	90 bp	At TSS Multiome	925
chr19:12,639,899–12,640,614	29.4 kb	Distal (>10kb) Multiome	454
chr19:12,647,538–12,648,022	36.9 kb	Distal (>10kb) Multiome	126
chr19:12,656,871–12,657,566	46.4 kb	Distal (>10kb) Multiome	254
chr19:12,666,317–12,667,225	56.0 kb	Distal (>10kb) Multiome	495
chr19:12,669,351–12,669,939	58.7 kb	Distal (>10kb) Multiome	777
chr19:12,681,003–12,682,117	70.6 kb	Distal (>10kb) Multiome	994
chr19:12,696,035–12,696,970	85.8 kb	Distal (>10kb) Multiome	806
chr19:12,702,968–12,703,602	92.4 kb	Distal (>10kb) Multiome	121
chr19:12,721,692–12,723,084	111.6 kb	Distal (>10kb) Multiome	807
chr19:12,723,726–12,724,142	113.3 kb	Distal (>10kb) Multiome	539
chr19:12,734,221–12,735,284	123.9 kb	Distal (>10kb) Multiome	882
chr19:12,736,470–12,737,780	126.3 kb	Distal (>10kb) Multiome	742
chr19:12,757,454–12,758,297	147.0 kb	Distal (>10kb) Multiome	588
chr19:12,765,876–12,766,545	155.5 kb	Distal (>10kb) Multiome	557
chr19:12,774,659–12,776,025	164.6 kb	Distal (>10kb) Multiome	803
chr19:12,777,481–12,778,589	167.1 kb	Distal (>10kb) Multiome	661
chr19:12,782,418–12,783,038	171.9 kb	Distal (>10kb) Multiome	699
chr19:12,789,543–12,790,654	179.2 kb	Distal (>10kb) Multiome	717
chr19:12,790,960–12,793,231	180.7 kb	Distal (>10kb) Multiome	1015
chr19:12,793,340–12,794,240	182.9 kb	Distal (>10kb) Multiome	808
chr19:12,801,120–12,802,290	191.1 kb	Distal (>10kb) Multiome	901
chr19:12,806,212–12,806,984	195.7 kb	Distal (>10kb) Multiome	827
chr19:12,825,565–12,826,186	215.0 kb	Distal (>10kb) Multiome	436
chr19:12,832,484–12,833,101	221.8 kb	Distal (>10kb) Multiome	970
chr19:12,833,638–12,834,477	223.1 kb	Distal (>10kb) Multiome	310
chr19:12,838,114–12,838,869	227.6 kb	Distal (>10kb) Multiome	377
chr19:12,840,071–12,841,485	230.0 kb	Distal (>10kb) Multiome	391
chr19:12,847,633–12,848,090	236.9 kb	Distal (>10kb) Multiome	535
chr19:12,867,327–12,868,022	256.8 kb	Distal (>10kb) Multiome	315
chr19:12,872,968–12,873,990	262.5 kb	Distal (>10kb) Multiome	263
chr19:12,880,834–12,881,875	270.7 kb	Distal (>10kb) Multiome	656
chr19:12,884,836–12,886,381	274.6 kb	Distal (>10kb) Multiome	717
chr19:12,890,614–12,891,603	280.2 kb	Distal (>10kb) Multiome	841

Genome Browser

Genomic view of the ZNF490 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.