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LOC115947634 CRISPRi-validated cis-regulatory element chr2.6880 [ Homo sapiens (human) ]

Gene ID: 115947634, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115947634
Gene description
CRISPRi-validated cis-regulatory element chr2.6880
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 CAB39 (calcium binding protein 39) gene on chromosome 2 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes three accessible chromatin subregions that were validated as enhancers based on their ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230658624..230659752)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231141733..231142861)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231523339..231524467)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17231 Neighboring gene tropomyosin 3 pseudogene 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17232 Neighboring gene RNA, U6 small nuclear 451, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17233 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17236 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231524789-231525345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17241 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231531133-231531998 Neighboring gene Sharpr-MPRA regulatory region 12127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17243 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17247 Neighboring gene formin-like protein 16 Neighboring gene long intergenic non-protein coding RNA 1907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12412 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231585879-231586402 Neighboring gene calcium binding protein 39 Neighboring gene BANF1 pseudogene 3

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
  4. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 17237
  • ATAC-STARR-seq lymphoblastoid active region 17238
  • ATAC-STARR-seq lymphoblastoid active region 17239

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_066577.1 

    Range
    101..1229
    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
    230658624..230659752
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    231141733..231142861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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