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LOC121587574 H3K4me1 hESC enhancers GRCh37_chr17:7754177-7755141 and GRCh37_chr17:7755142-7756105 [ Homo sapiens (human) ]

Gene ID: 121587574, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587574
Gene description
H3K4me1 hESC enhancers GRCh37_chr17:7754177-7755141 and GRCh37_chr17:7755142-7756105
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 marked by the H3K4me1 histone modification were validated as active enhancers by ChIP-STARR-seq in naive human embryonic stem cells. 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 25:Art, potential CNV or repetitive artifacts). 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, May 2023]
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Genomic context

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Location:
17p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7850859..7852787)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7756183..7758111)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7755029..7755323)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 2 Neighboring gene ribosomal protein L29 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7736627-7737238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7737869-7738368 Neighboring gene translation initiation factor IF-2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7742757-7743257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11647 Neighboring gene lysine demethylase 6B Neighboring gene uncharacterized LOC107987244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7756106-7757070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7759303-7759840 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11650 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7760574-7761436 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7761437-7762298 Neighboring gene transmembrane protein 88 Neighboring gene cytochrome b5 domain containing 1 Neighboring gene N-alpha-acetyltransferase 38, NatC auxiliary subunit

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 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 11648
  • ATAC-STARR-seq lymphoblastoid active region 11649
  • H3K4me1 hESC enhancer GRCh37_chr17:7754177-7755141
  • H3K4me1 hESC enhancer GRCh37_chr17:7755142-7756105
  • Sharpr-MPRA regulatory region 3930

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_074862.2 

    Range
    101..2029
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    7850859..7852787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    7756183..7758111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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