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LOC112590813 Sharpr-MPRA regulatory region 11871 [ Homo sapiens (human) ]

Gene ID: 112590813, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112590813
Gene description
Sharpr-MPRA regulatory region 11871
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 DNase matched - State 1:Tss, active promoter, TSS/CpG island region). The same subregion also displayed repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Jan 2023]
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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 (6127057..6128003)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (5652744..5653690)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (6187769..6188063)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5939868-5940372 Neighboring gene nephrocystin 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5956455-5957256 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5957257-5958056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5968773-5969298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5979954-5980454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5999651-6000151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6004026-6004526 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6009504-6009801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6027103-6027602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6031677-6032176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6051054-6051908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 70 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6059331-6060045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6060046-6060760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6062904-6063618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6068670-6069262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6070973-6071474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6072741-6073242 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6084854-6085618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 71 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6086382-6087145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 73 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 74 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6113495-6113995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6120127-6120627 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:6133526-6134725 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6143081-6143561 Neighboring gene uncharacterized LOC124903831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6162189-6162690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6162691-6163190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6186229-6187116 Neighboring gene chromodomain helicase DNA binding protein 5 Neighboring gene MPRA-validated peak27 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6225727-6226227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6238637-6239138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6239139-6239638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 138 Neighboring gene Sharpr-MPRA regulatory region 5942 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6265555-6266374 Neighboring gene RNF207 antisense RNA 1 Neighboring gene ribosomal protein L22

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_chr1:6187117-6188006

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_060603.2 

    Range
    101..1047
    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
    6127057..6128003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    5652744..5653690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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