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LOC120893135 Sharpr-MPRA regulatory region 5491 [ Homo sapiens (human) ]

Gene ID: 120893135, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120893135
Gene description
Sharpr-MPRA regulatory region 5491
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. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53444596..53444890)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53326835..53327129)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53910269..53910563)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2812 Neighboring gene hESC enhancers GRCh37_chr1:53858569-53859069 and GRCh37_chr1:53859129-53859812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53862275-53863150 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53863151-53864025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53874144-53874739 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:53895322-53895839 Neighboring gene MPRA-validated peak233 silencer Neighboring gene uncharacterized LOC105378733 Neighboring gene solute carrier family 25 member 3 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53928578-53929106 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53934837-53935376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53935377-53935914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53949500-53950120 Neighboring gene DMRT like family B with proline rich C-terminal 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53966190-53967030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53969230-53969793 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53972264-53972790 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53972791-53973317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53992273-53992776 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53993281-53993784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54005067-54006034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54006035-54007002 Neighboring gene GLIS family zinc finger 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54011803-54012302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54042179-54042808 Neighboring gene MPRA-validated peak234 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr1:54082618-54082784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54086231-54086735 Neighboring gene Sharpr-MPRA regulatory region 11088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54150404-54151233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54151234-54152062 Neighboring gene RNA, U7 small nuclear 95 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

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)

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_073894.1 

    Range
    101..395
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    53444596..53444890
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    53326835..53327129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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