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LOC116216121 CRISPRi-validated cis-regulatory element chr10.4148 [ Homo sapiens (human) ]

Gene ID: 116216121, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116216121
Gene description
CRISPRi-validated cis-regulatory element chr10.4148
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 cis-regulatory element for the PDCD4 (programmed cell death 4) gene on chromosome 10 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (110857585..110857954)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (111741361..111741730)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (112617343..112617712)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 20 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112523918-112524418 Neighboring gene RN7SK pseudogene 288 Neighboring gene RNA, 5S ribosomal pseudogene 327 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:112534241-112535440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112571707-112572272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4043 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:112589780-112589960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:112605645-112606144 Neighboring gene uncharacterized LOC124902499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4053 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112619133-112619632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4054 Neighboring gene uncharacterized LOC124902500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:112630184-112630794 Neighboring gene PDCD4 antisense RNA 1

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

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 active region 4052

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_066888.1 

    Range
    101..470
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    110857585..110857954
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    111741361..111741730
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
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