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LOC112590805 hESC enhancers GRCh37_chr1:53858569-53859069 and GRCh37_chr1:53859129-53859812 [ Homo sapiens (human) ]

Gene ID: 112590805, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112590805
Gene description
hESC enhancers GRCh37_chr1:53858569-53859069 and GRCh37_chr1:53859129-53859812
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. Two subregions were validated as active enhancers by ChIP-STARR-seq in primed human embryonic stem cells, where both subregions were marked by the H3K4me1 histone modification and one was additionally marked by H3K27ac. An overlapping subregion was also 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 unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 12:CtcfO). An accessible chromatin subregion was used in a lentiviral ReSE (repressive ability of silencer elements) screen that assays for cell survival based on transcriptional repression of an apoptosis-inducing fusion protein. That subregion was identified as a functional silencer 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) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC112590805 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53392897..53394140)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53275130..53276375)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53859049..53859343)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378731 Neighboring gene LRP8 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53805229-53805730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1047 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:53816803-53817658 Neighboring gene long intergenic non-protein coding RNA 2812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53862275-53863150 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53863151-53864025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53874144-53874739 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:53895322-53895839 Neighboring gene MPRA-validated peak233 silencer Neighboring gene uncharacterized LOC105378733 Neighboring gene solute carrier family 25 member 3 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 5491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53928578-53929106 Neighboring gene DMRT like family B with proline rich C-terminal 1

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. Systematic identification of silencers in human cells. Pang B, et al. Nat Genet, 2020 Mar. PMID 32094911, Free PMC Article
  2. 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
  3. 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
  4. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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 1048
  • ATAC-STARR-seq lymphoblastoid active region 1049
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53859129-53859812
  • H3K4me1 hESC enhancer GRCh37_chr1:53858569-53859069
  • ReSE screen-validated silencer GRCh37_chr1:53859028-53859257
  • Sharpr-MPRA regulatory region 1525

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_060595.2 

    Range
    101..1344
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    53392897..53394140
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    53275130..53276375
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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