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LOC116268430 CRISPRi-validated cis-regulatory element chr12.444 [ Homo sapiens (human) ]

Gene ID: 116268430, updated on 12-Sep-2024

Summary

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Gene symbol
LOC116268430
Gene description
CRISPRi-validated cis-regulatory element chr12.444
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 SLC2A3 (solute carrier family 2 member 3) gene on chromosome 12 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 LOC116268430 in Genome Data Viewer
Location:
12p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7959811..7959936)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7973969..7974094)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (8112407..8112532)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene Nanog homeobox pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:8057929-8058458 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8060583-8061114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8062177-8062706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8065488-8066477 Neighboring gene solute carrier family 2 member 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8086891-8087844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4205 Neighboring gene CRISPRi-validated cis-regulatory element chr12.441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5923 Neighboring gene CRISPRi-validated cis-regulatory element chr12.445 Neighboring gene uncharacterized LOC124902871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8120522-8121234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8121235-8121947 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8123373-8124086 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:8134452-8135651 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:8145332-8146221 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8147335-8148256 Neighboring gene ribosomal protein S20 pseudogene 28

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_066945.1 

    Range
    101..226
    Download
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    7959811..7959936
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    7973969..7974094
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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