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LOC116268478 CRISPRi-validated cis-regulatory element chr15.3129 [ Homo sapiens (human) ]

Gene ID: 116268478, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116268478
Gene description
CRISPRi-validated cis-regulatory element chr15.3129
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 both the HAPLN3 (hyaluronan and proteoglycan link protein 3) and MFGE8 (milk fat globule-EGF factor 8 protein) genes on chromosome 15 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2019]
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Genomic context

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See LOC116268478 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (88987086..88987305)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (86741982..86742201)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (89530317..89530536)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene non-histone chromosomal protein HMG-14-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10038 Neighboring gene MPRA-validated peak2417 silencer Neighboring gene keratin 18 pseudogene 47 Neighboring gene MPRA-validated peak2418 silencer Neighboring gene CRISPRi-validated cis-regulatory element chr15.3128 Neighboring gene capping actin protein of muscle Z-line subunit alpha 2 pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:89536398-89537299 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:89542092-89542895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:89545400-89546011 Neighboring gene Sharpr-MPRA regulatory region 4646 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:89547127-89547627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89574853-89575354 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:89592211-89592762 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:89602566-89603066 Neighboring gene coronary artery disease region linked MFGE8 regulatory lncRNA Neighboring gene abhydrolase domain containing 2, acylglycerol lipase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10040

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_066993.1 

    Range
    101..320
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    88987086..88987305
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    86741982..86742201
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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