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LOC116276508 CRISPRi-validated cis-regulatory element chr19.2871 [ Homo sapiens (human) ]

Gene ID: 116276508, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276508
Gene description
CRISPRi-validated cis-regulatory element chr19.2871
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. A subregion was validated as a high-confidence cis-regulatory element for the JUND (JunD proto-oncogene, AP-1 transcription factor subunit) gene on chromosome 19 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. Another subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC116276508 in Genome Data Viewer
Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18289990..18290647)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18424102..18424759)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18401089..18401457)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18391566-18392417 Neighboring gene uncharacterized LOC124904652 Neighboring gene microRNA 3188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18398502-18399345 Neighboring gene ribosomal protein L39 pseudogene 38 Neighboring gene uncharacterized LOC124904653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10385 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18404637-18405276 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18405513-18405695 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2873 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18415779-18416284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18417751-18418708 Neighboring gene LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18425352-18425852 Neighboring gene uncharacterized LOC105372300 Neighboring gene Sharpr-MPRA regulatory region 14103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18429424-18430170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14313 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:18434425-18435027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14314 Neighboring gene uncharacterized LOC124904654 Neighboring gene RNA, 7SL, cytoplasmic 513, pseudogene

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. 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

  • H3K4me1 hESC enhancer GRCh37_chr19:18400800-18401439

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_067059.2 

    Range
    101..758
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    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    18289990..18290647
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18424102..18424759
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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