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LOC116216103 CRISPRi-validated cis-regulatory element chr9.4291 [ Homo sapiens (human) ]

Gene ID: 116216103, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116216103
Gene description
CRISPRi-validated cis-regulatory element chr9.4291
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region represents a DNase I hypersensitive site (DHS) that was predicted to be an enhancer by the ENCODE (ENCyclopedia Of DNA Elements) project based on various combinations of H3K27 acetylation and binding of p300, GATA1 and RNA polymerase II in K562 erythroleukemia cells. The major subregion was validated as a cis-regulatory element for the EGFL7 (EGF like domain multiple 7) gene on chromosome 9 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were shown to be active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. This locus also includes four accessible chromatin subregions that were validated as silencers based on their ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136644323..136647057)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148877305..148880039)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139538775..139541484)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139473242-139473768 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139479375-139480026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139493297-139493830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139494899-139495430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139495673-139496524 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:139499139-139499319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139499925-139500774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139501625-139502474 Neighboring gene Sharpr-MPRA regulatory region 9516 Neighboring gene long intergenic non-protein coding RNA 1451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139524155-139524686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139525219-139525750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139525751-139526282 Neighboring gene uncharacterized LOC105376325 Neighboring gene uncharacterized LOC102724193 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139549554-139550178 Neighboring gene uncharacterized LOC101928612 Neighboring gene EGF like domain multiple 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139563885-139564386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139564387-139564886 Neighboring gene microRNA 126

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  2. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  4. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  5. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 20531
  • ATAC-STARR-seq lymphoblastoid silent region 20532
  • ATAC-STARR-seq lymphoblastoid silent region 20533
  • ATAC-STARR-seq lymphoblastoid silent region 20534
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139540115-139540812
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139540813-139541509

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_066870.2 

    Range
    101..2835
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    136644323..136647057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    148877305..148880039
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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