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LOC115804242 CRISPRi-validated cis-regulatory element chr1.10803 [ Homo sapiens (human) ]

Gene ID: 115804242, updated on 10-Dec-2024

Summary

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Gene symbol
LOC115804242
Gene description
CRISPRi-validated cis-regulatory element chr1.10803
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 TMEM183A (transmembrane protein 183A) gene on chromosome 1 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 primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac histone modification. [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC115804242 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (203005177..203006052)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (202267884..202268759)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202974305..202975180)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1713 Neighboring gene Sharpr-MPRA regulatory region 11869 Neighboring gene cytochrome b5 reductase 1 Neighboring gene MGAT4 family member F, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:202975854-202976628 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:202976629-202977401 Neighboring gene ribosomal protein S20 pseudogene 8 Neighboring gene transmembrane protein 183A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202995545-202996066 Neighboring gene PTPRF interacting protein alpha 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203010223-203010724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203010725-203011224 Neighboring gene Sharpr-MPRA regulatory region 9252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203013943-203014581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203014582-203015219 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:203015372-203015574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203017091-203017988 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203020635-203021176 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:203023677-203024428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203024429-203025180 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:203030137-203030721 Neighboring gene uncharacterized LOC105371687

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

  • NANOG-H3K27ac hESC enhancer GRCh37_chr1:202974305-202975079

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_066125.2 

    Range
    101..976
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    203005177..203006052
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    202267884..202268759
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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