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LOC127823033 CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128480315-128481964 [ Homo sapiens (human) ]

Gene ID: 127823033, updated on 10-Oct-2023

Summary

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Gene symbol
LOC127823033
Gene description
CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128480315-128481964
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 was predicted to be an enhancer based on an activity-by-contact (ABC) model that predicts enhancer-gene connections, where the putative enhancer strength is measured by DNase I hypersensitivity and H3K27 acetylation, and the contact frequency by Hi-C. It was validated as a positively-acting cis-regulatory element for the ETS1 (ETS proto-oncogene 1, transcription factor) gene based on CRISPR/Cas9-mediated perturbation (CRISPRi-FlowFISH method) in GM12878 lymphoblastoid cells. A subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its 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 cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC127823033 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (128610420..128612069)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (128643674..128645323)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ETS proto-oncogene 1, transcription factor Neighboring gene uncharacterized LOC124902790 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:128401737-128402434 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:128402435-128403132 Neighboring gene NANOG hESC enhancer GRCh37_chr11:128403302-128403803 Neighboring gene NANOG hESC enhancer GRCh37_chr11:128420904-128421445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5724 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5725 Neighboring gene CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128422800-128423300 Neighboring gene uncharacterized LOC105369565 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128446088-128446588 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:128452292-128453010 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:128453011-128453727 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:128457406-128457612 Neighboring gene uncharacterized LOC105369568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128485091-128485590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128485724-128486224 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:128491606-128492805 Neighboring gene CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128494058-128494944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128523817-128524317 Neighboring gene uncharacterized LOC101929538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4058 Neighboring gene CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128563455-128564187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4061 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4062 Neighboring gene Fli-1 proto-oncogene, ETS transcription factor Neighboring gene smooth muscle and endothelial cell enriched migration/differentiation-associated lncRNA

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-wide enhancer maps link risk variants to disease genes. Nasser J, et al. Nature, 2021 May. PMID 33828297, Free PMC Article
  2. 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
  3. 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 5729
  • H3K4me1 hESC enhancer GRCh37_chr11:128480578-128481121

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_124472.2 

    Range
    101..1750
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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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    128610420..128612069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    128643674..128645323
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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