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LOC121587578 Sharpr-MPRA regulatory region 10806 [ Homo sapiens (human) ]

Gene ID: 121587578, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121587578
Gene description
Sharpr-MPRA regulatory region 10806
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 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 (17784567..17785209)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17731181..17731823)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17688229..17688523)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene retinoic acid induced 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17665979-17666591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17666592-17667203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11810 Neighboring gene RAI1 antisense RNA 1 Neighboring gene uncharacterized LOC124903942 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17682070-17682959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17683849-17684738 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17685874-17686374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17687340-17687880 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17693241-17693447 Neighboring gene Smith-Magenis syndrome chromosome region, candidate 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17696322-17697048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17697049-17697773 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17704013-17704802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17704803-17705590 Neighboring gene Sharpr-MPRA regulatory region 10333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8256 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17716071-17716629 Neighboring gene sterol regulatory element binding transcription factor 1 Neighboring gene microRNA 6777 Neighboring gene microRNA 33b

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. 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

  • H3K4me1 hESC enhancer GRCh37_chr17:17687881-17688419

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_074866.2 

    Range
    101..743
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    17784567..17785209
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    17731181..17731823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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