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LOC112577530 Sharpr-MPRA regulatory region 2190 [ Homo sapiens (human) ]

Gene ID: 112577530, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577530
Gene description
Sharpr-MPRA regulatory region 2190
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 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 non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC112577530 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (201888391..201889035)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201146146..201146790)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (201857869..201858163)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene neuron navigator 1 Neighboring gene IPO9 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201796884-201797398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201797399-201797912 Neighboring gene Sharpr-MPRA regulatory region 13839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2322 Neighboring gene microRNA 1231 Neighboring gene Sharpr-MPRA regulatory region 12270 Neighboring gene Sharpr-MPRA regulatory region 11581 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:201837758-201837973 Neighboring gene importin 9 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201851435-201851934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2323 Neighboring gene microRNA 6739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201883337-201883837 Neighboring gene shisa family member 4 Neighboring gene leiomodin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:201910579-201911528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2325 Neighboring gene translocase of inner mitochondrial membrane 17A

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_chr1:201857519-201858028

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_060449.2 

    Range
    101..745
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    201888391..201889035
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    201146146..201146790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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