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LOC120893176 Sharpr-MPRA regulatory region 9898 [ Homo sapiens (human) ]

Gene ID: 120893176, updated on 12-Sep-2024

Summary

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Gene symbol
LOC120893176
Gene description
Sharpr-MPRA regulatory region 9898
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. A subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in primed 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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). 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 lymphoblastoid cells. [provided by RefSeq, Jun 2023]
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Genomic context

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See LOC120893176 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (205591881..205592755)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (204856424..204857297)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (205561009..205561883)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205475721-205476374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205479231-205479778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205480776-205481390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205484536-205485236 Neighboring gene cyclin dependent kinase 18 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:205486639-205487338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205490554-205491379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205505565-205506066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1743 Neighboring gene Sharpr-MPRA regulatory region 5902 Neighboring gene MFSD4A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205538423-205538972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205538973-205539521 Neighboring gene RNA, U2 small nuclear 19, pseudogene Neighboring gene major facilitator superfamily domain containing 4A Neighboring gene uncharacterized LOC124904491 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2381 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205555399-205556189 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:205569093-205570292 Neighboring gene RNA, U6 small nuclear 418, pseudogene Neighboring gene ETS transcription factor ELK4 Neighboring gene GABA type A receptor-associated protein pseudogene

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
  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 2382
  • H3K4me1 hESC enhancer GRCh37_chr1:205561383-205561883

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_073935.2 

    Range
    101..975
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    205591881..205592755
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    204856424..204857297
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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