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LOC116276493 CRISPRi-validated cis-regulatory element chr19.73 [ Homo sapiens (human) ]

Gene ID: 116276493, updated on 10-Oct-2023

Summary

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Gene symbol
LOC116276493
Gene description
CRISPRi-validated cis-regulatory element chr19.73
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 BSG (basigin (Ok blood group)) gene on chromosome 19 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:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (555762..557000)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (509936..511174)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (555762..557000)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:531801-532457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:534117-534693 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:534694-535269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13563 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:535719-535880 Neighboring gene cell division cycle 34, ubiqiutin conjugating enzyme Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:543421-544066 Neighboring gene granzyme M Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:570844-571416 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13564 Neighboring gene BSG antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9607 Neighboring gene basigin (Ok blood group) Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:583377-583939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:583940-584501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:588071-588650 Neighboring gene Rho GTPase activating protein 33 pseudogene Neighboring gene hyperpolarization activated cyclic nucleotide gated potassium and sodium channel 2

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_067044.1 

    Range
    101..1339
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    555762..557000
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    509936..511174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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