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LOC115995538 CRISPRi-validated cis-regulatory element chr3.5817 [ Homo sapiens (human) ]

Gene ID: 115995538, updated on 10-Oct-2023

Summary

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Gene symbol
LOC115995538
Gene description
CRISPRi-validated cis-regulatory element chr3.5817
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 TFRC (transferrin receptor) gene on chromosome 3 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. This locus also includes two 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:
3q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (196193787..196194446)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (198913349..198914008)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (195920658..195921317)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene transferrin receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15051 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195807213-195807712 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15052 Neighboring gene RNA, U7 small nuclear 18 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15053 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:195812346-195812518 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:195819312-195819500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15054 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:195840246-195840363 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15055 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:195853055-195853556 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:195861292-195861451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195862621-195863421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21067 Neighboring gene long intergenic non-protein coding RNA 885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21071 Neighboring gene CRISPRi-validated cis-regulatory element chr3.5812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195913396-195914015 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195914016-195914634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:195917731-195918349 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195919335-195919998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195924959-195925904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195929545-195930080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195930123-195930624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195930625-195931124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15058 Neighboring gene zinc finger DHHC-type palmitoyltransferase 19 Neighboring gene uncharacterized LOC124909479 Neighboring gene uncharacterized LOC105374304

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 21074
  • ATAC-STARR-seq lymphoblastoid active region 21075

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_066619.1 

    Range
    101..760
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    196193787..196194446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    198913349..198914008
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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