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LOC112577598 Sharpr-MPRA regulatory region 6057 [ Homo sapiens (human) ]

Gene ID: 112577598, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112577598
Gene description
Sharpr-MPRA regulatory region 6057
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 both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jun 2018]
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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 (39899017..39899311)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (39768457..39768751)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (40364689..40364983)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378667 Neighboring gene MPRA-validated peak189 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 822 Neighboring gene tRNA isopentenyltransferase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40348408-40349228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40349229-40350047 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:40353876-40354074 Neighboring gene MYCL antisense RNA 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:40363871-40364442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 716 Neighboring gene MYCL proto-oncogene, bHLH transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:40409912-40410434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 823 Neighboring gene MFSD2 lysolipid transporter A, lysophospholipid Neighboring gene ribosomal protein S2 pseudogene 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40446045-40446898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 718 Neighboring gene uncharacterized LOC105378669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 824 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40505419-40506052 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:40506053-40506687 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 1

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_060530.1 

    Range
    101..395
    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
    39899017..39899311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    39768457..39768751
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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