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LOC116268449 CRISPRi-validated cis-regulatory element chr12.3595 [ Homo sapiens (human) ]

Gene ID: 116268449, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116268449
Gene description
CRISPRi-validated cis-regulatory element chr12.3595
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 C12orf76 (chromosome 12 open reading frame 76) 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 LOC116268449 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (110118384..110118655)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (110094157..110094428)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (110556189..110556460)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110480304-110480817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6993 Neighboring gene chromosome 12 open reading frame 76 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6995 Neighboring gene CRISPRi-validated cis-regulatory element chr12.3588 Neighboring gene uncharacterized LOC105369976 Neighboring gene Sharpr-MPRA regulatory region 13461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110546777-110547368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110547369-110547960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4853 Neighboring gene intraflagellar transport 81 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110610112-110610892 Neighboring gene MPRA-validated peak1945 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110661551-110662051 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110695091-110695683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110706905-110707507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4854 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110719747-110720501 Neighboring gene ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6999 Neighboring gene Sharpr-MPRA regulatory region 3729 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7000 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:110778306-110779505 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:110782389-110783588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:110786998-110787545

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_066964.1 

    Range
    101..372
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    110118384..110118655
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    110094157..110094428
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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