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LOC115945161 CRISPRi-validated cis-regulatory element chr2.2721 [ Homo sapiens (human) ]

Gene ID: 115945161, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115945161
Gene description
CRISPRi-validated cis-regulatory element chr2.2721
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 EMX1 (empty spiracles homeobox 1) gene on chromosome 2 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:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (72901285..72902066)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (72914229..72915010)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (73128414..73129195)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene exocyst complex component 6B Neighboring gene small nucleolar RNA SNORD78 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72999013-72999514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72999515-73000014 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:73052157-73052667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11625 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:73110580-73110740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11626 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:73115417-73115591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73119309-73119810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16022 Neighboring gene VISTA enhancer hs1025 Neighboring gene zinc finger MYM-type containing 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73144013-73144629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73143395-73144012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73164255-73164932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73165285-73165786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73168998-73169986 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73177717-73178218 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73177215-73177716 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73178721-73179222 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73179223-73179724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73186243-73186743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:73191385-73192078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73192079-73192770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:73209618-73210118 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:73216229-73216428 Neighboring gene sepiapterin reductase Neighboring gene Sharpr-MPRA regulatory region 2442 Neighboring gene uncharacterized LOC107985897 Neighboring gene empty spiracles homeobox 1 Neighboring gene sideroflexin 5

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_066561.1 

    Range
    101..882
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    72901285..72902066
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    72914229..72915010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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