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LOC116183082 CRISPRi-validated cis-regulatory element chr7.769 [ Homo sapiens (human) ]

Gene ID: 116183082, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116183082
Gene description
CRISPRi-validated cis-regulatory element chr7.769
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. It was validated as a high-confidence cis-regulatory element for the FSCN1 (fascin actin-bundling protein 1) gene on chromosome 7 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. A subregion was also shown to be an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Dec 2022]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (5574187..5575298)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (5691708..5692819)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (5613818..5614929)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5567118-5567988 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5567989-5568858 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5568859-5569728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5573209-5574078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5586399-5586898 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5593001-5593846 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5594693-5595538 Neighboring gene actin beta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5595539-5596384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5597701-5598249 Neighboring gene S100 calcium binding protein A11 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5601490-5602016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5602017-5602541 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5602542-5603067 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5609174-5610162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5626381-5626880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17926 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:5633617-5634192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17928 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:5634770-5635345 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:5636965-5637180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5642390-5643243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5643244-5644096 Neighboring gene Sharpr-MPRA regulatory region 1133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5648079-5648632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5655393-5656132 Neighboring gene fascin actin-bundling protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:5666829-5667500 Neighboring gene VISTA enhancer hs1623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:5678992-5679856 Neighboring gene ring finger protein 216 Neighboring gene RNF216 intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25605

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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  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

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:5614301-5614868

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_066810.1 

    Range
    101..1212
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    5574187..5575298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    5691708..5692819
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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