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LOC115995504 CRISPRi-validated cis-regulatory element chr3.91 [ Homo sapiens (human) ]

Gene ID: 115995504, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995504
Gene description
CRISPRi-validated cis-regulatory element chr3.91
Gene type
biological region
Feature type(s)
regulatory: 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 BHLHE40 (basic helix-loop-helix family member e40) gene on chromosome 3 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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Genomic context

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See LOC115995504 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (5021829..5022027)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (5015602..5015800)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (5063514..5063712)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906209 Neighboring gene small nucleolar RNA U13 Neighboring gene BHLHE40 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:4947837-4948542 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:4958477-4959105 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:4987703-4987867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19366 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:5021511-5022105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5024435-5024994 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5024995-5025554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5027373-5028270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5028271-5029168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5030786-5031286 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5036716-5037915 Neighboring gene basic helix-loop-helix family member e40 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:5043965-5044466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19373 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5054312-5055114 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:5055115-5055916 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:5064405-5065604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5073333-5073834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19375 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:5119481-5119626 Neighboring gene ring finger protein 10 pseudogene 1 Neighboring gene UBTF like 8 (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

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)

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_066585.1 

    Range
    101..299
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    5021829..5022027
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    5015602..5015800
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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