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LOC116158548 CRISPRi-validated cis-regulatory element chr6.1077 [ Homo sapiens (human) ]

Gene ID: 116158548, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116158548
Gene description
CRISPRi-validated cis-regulatory element chr6.1077
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 H1-3 (H1.3 linker histone, cluster member) and H1-4 (H1.4 linker histone, cluster member) genes on chromosome 6, and with lower confidence for the H4C3 (H4 clustered histone 3) gene, 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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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (25958670..25958974)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (25824573..25824877)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (25958898..25959202)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H2B histone pseudogene 5 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:25898344-25898933 Neighboring gene solute carrier family 17 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24170 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:25971247-25972446 Neighboring gene tripartite motif containing 38 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24171 Neighboring gene long intergenic non-protein coding RNA 2980 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:25999111-25999745 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:25999746-26000381

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 1.1-Mb transcript map of the hereditary hemochromatosis locus. Ruddy DA, et al. Genome Res, 1997 May. PMID 9149941
  2. 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
  3. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  4. 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_066760.1 

    Range
    101..405
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    25958670..25958974
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    25824573..25824877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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