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LOC121132684 Sharpr-MPRA regulatory region 10128 [ Homo sapiens (human) ]

Gene ID: 121132684, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121132684
Gene description
Sharpr-MPRA regulatory region 10128
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. 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 HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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See LOC121132684 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (43070051..43070345)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42898796..42899090)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (43037789..43038083)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901318 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:43013559-43013750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43018382-43018882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43018883-43019383 Neighboring gene cullin 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43019933-43020768 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24587 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:43027385-43028336 Neighboring gene mitochondrial ribosomal protein L2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43038920-43039420 Neighboring gene kinesin light chain 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43043187-43043710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17218 Neighboring gene KLC4 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:43049243-43049446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43050481-43051047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43051048-43051613 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43057365-43057958 Neighboring gene protein tyrosine kinase 7 (inactive) Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:43057959-43058553 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43058554-43059147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24591 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43086921-43087840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43087841-43088760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43099803-43100304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43100305-43100804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24592

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_074226.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    43070051..43070345
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    42898796..42899090
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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