ZNF639

zinc finger protein 639 | ANC-2H01, ZASC1

This gene encodes a member of the Kruppel-like zinc finger family of proteins. Amplification and overexpression of this gene have been observed in esophageal squamous cell carcinoma. The encoded protein has been shown to bind DNA in a sequence-specific manner and may regulate HIV-1 gene expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

Member of: DE-7 Developmental clusters: GC4

Biological processes 18 terms

DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)host-mediated activation of viral transcription (GO:0043923)host-mediated suppression of viral transcription (GO:0043922)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of DNA-templated transcription (GO:0045892)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of cell growth (GO:0030307)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)regulation of transcription by RNA polymerase II (GO:0006357)symbiont entry into host cell (GO:0046718)transcription cis-regulatory region binding (GO:0000976)

Expression (TPM)

TFs regulating ZNF639 0 TFs

Transcription factors with Perturb-seq knockdown data for ZNF639. 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 = ZNF639 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 ZNF639

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of ZNF639, 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
chr3:179,071,152–179,072,483	251.2 kb	Distal (>10kb) Multiome HiCAR	794
chr3:179,147,033–179,149,466	174.8 kb	Distal (>10kb) Multiome	953
chr3:179,260,956–179,261,810	61.6 kb	Distal (>10kb) Multiome	616
chr3:179,315,877–179,316,305	6.7 kb	Proximal (<10kb)	202
chr3:179,321,681–179,322,234	795 bp	At TSS	164
chr3:179,322,380–179,323,876	54 bp	At TSS Multiome	958
chr3:179,324,601–179,324,723	1.6 kb	Proximal (<10kb)	70
chr3:179,346,338–179,348,224	24.6 kb	Distal (>10kb) Multiome	843
chr3:179,450,888–179,452,034	128.5 kb	Distal (>10kb) Multiome	580
chr3:179,504,159–179,505,204	181.6 kb	Distal (>10kb) Multiome	128
chr3:179,526,783–179,527,418	204.1 kb	Distal (>10kb) Multiome	358
chr3:179,562,395–179,564,138	239.8 kb	Distal (>10kb) Multiome	866
chr3:179,604,200–179,605,304	281.7 kb	Distal (>10kb) Multiome	786
chr3:179,608,248–179,609,637	285.8 kb	Distal (>10kb) Multiome	176

Genome Browser

Genomic view of the ZNF639 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.