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LOC116276447 CRISPRi-validated cis-regulatory element chr16.1224 [ Homo sapiens (human) ]

Gene ID: 116276447, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276447
Gene description
CRISPRi-validated cis-regulatory element chr16.1224
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 ATF7IP2 (activating transcription factor 7 interacting protein 2) gene on chromosome 16 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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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (11231374..11231670)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (11267600..11267896)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (11325231..11325527)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene C-type lectin domain containing 16A Neighboring gene uncharacterized LOC105371081 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234584-11235161 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11234005-11234583 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11235162-11235740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11238795-11239462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11268031-11268544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11275481-11276366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11276367-11277253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11291308-11291816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11290798-11291307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11292853-11293353 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:11295121-11296320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:11296313-11297109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11304646-11305240 Neighboring gene uncharacterized LOC107984859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10423 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10425 Neighboring gene Sharpr-MPRA regulatory region 4189 Neighboring gene uncharacterized LOC105371082 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11344039-11344246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7200 Neighboring gene heterogeneous nuclear ribonucleoprotein C pseudogene 4 Neighboring gene suppressor of cytokine signaling 1

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_066998.1 

    Range
    101..397
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    11231374..11231670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    11267600..11267896
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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