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LOC121294076 Sharpr-MPRA regulatory region 3596 [ Homo sapiens (human) ]

Gene ID: 121294076, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121294076
Gene description
Sharpr-MPRA regulatory region 3596
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC121294076 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (22909016..22909310)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (23183621..23183915)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (22766529..22766823)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene phosphatidylethanolamine binding protein 4 Neighboring gene uncharacterized LOC101929237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22744265-22744765 Neighboring gene uncharacterized LOC124901907 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:22760306-22760493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22769137-22769908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22769909-22770680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22777059-22777987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22809645-22810276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22810277-22810907 Neighboring gene uncharacterized LOC107984124 Neighboring gene NANOG hESC enhancer GRCh37_chr8:22814761-22815262 Neighboring gene VISTA enhancer hs1927 Neighboring gene Rho related BTB domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27100 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22845205-22845961 Neighboring gene RNA, 7SL, cytoplasmic 303, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22861268-22861793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22861794-22862318 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr8:22866186-22866771 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22871840-22872604 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:22876025-22876192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22876488-22877052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22877053-22877615 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:22885758-22886258 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:22886259-22886759 Neighboring gene TNF receptor superfamily member 10b Neighboring gene Sharpr-MPRA regulatory region 6582 Neighboring gene TNFRSF10B antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:22921484-22922683 Neighboring gene TNFRSF10B 5' regulatory region

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 19016

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_074318.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    22909016..22909310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    23183621..23183915
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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