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LOC115804258 CRISPRi-validated cis-regulatory element chr2.184 [ Homo sapiens (human) ]

Gene ID: 115804258, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115804258
Gene description
CRISPRi-validated cis-regulatory element chr2.184
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 ID2 (inhibitor of DNA binding 2) gene on chromosome 2 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Sep 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 (8534651..8535653)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (8558309..8559311)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (8674781..8675783)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 298 Neighboring gene uncharacterized LOC124907727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8160164-8160664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8160665-8161165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8168595-8169096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8169097-8169596 Neighboring gene long intergenic non-protein coding RNA 299 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:8226605-8227804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8289994-8290494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8290495-8290995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8299141-8299642 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:8299609-8299785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8329342-8329842 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:8333701-8334276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15252 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8393901-8394772 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:8403947-8404533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8417861-8418362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8421562-8422062 Neighboring gene NANOG hESC enhancer GRCh37_chr2:8440800-8441356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15255 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8532754-8533299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8580531-8581030 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:8587230-8588429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8635675-8636175 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11124 Neighboring gene CRISPRi-validated cis-regulatory element chr2.183 Neighboring gene CRISPRi-validated cis-regulatory element chr2.185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8684355-8684861 Neighboring gene Sharpr-MPRA regulatory region 11674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8683848-8684354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15265 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8712051-8712630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15272 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8723860-8724539 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8724540-8725218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8727462-8728114 Neighboring gene long intergenic non-protein coding RNA 1814 Neighboring gene uncharacterized LOC105373411 Neighboring gene SNRPE pseudogene 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_066141.1 

    Range
    101..1103
    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
    8534651..8535653
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    8558309..8559311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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