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LOC123744832 Sharpr-MPRA regulatory region 9523 [ Homo sapiens (human) ]

Gene ID: 123744832, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123744832
Gene description
Sharpr-MPRA regulatory region 9523
Gene type
biological region
Feature type(s)
regulatory: 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 repressive element 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 Repressive DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123744832 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (60428964..60429258)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (61596417..61596711)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (57396709..57397003)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene SUMO specific peptidase 6 pseudogene Neighboring gene RBBP4 pseudogene 4 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:58773583-58774340 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:58774341-58775097 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58775889-58776446 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58776447-58777002 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58777003-58777558 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58777559-58778114 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58778115-58778671 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58778672-58779227 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:58779228-58779784 Neighboring gene NANOG hESC enhancer GRCh37_chr6:57337645-57338146 Neighboring gene NANOG hESC enhancer GRCh37_chr6:57339131-57339632 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:57354999-57355730 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:57356812-57357419 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:57356203-57356811 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:57380456-57381014 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:57383839-57384752 Neighboring gene primase 2B, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:57515883-57517082 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:57525190-57526389 Neighboring gene NANOG hESC enhancer GRCh37_chr6:57538278-57538779 Neighboring gene NANOG hESC enhancer GRCh37_chr6:57579775-57580276 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:57638823-57639671 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:57811262-57811857 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 41 Neighboring gene RBBP4 pseudogene 3

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_078132.1 

    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
    60428964..60429258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    61596417..61596711
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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