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LOC123466219 Sharpr-MPRA regulatory region 6001 [ Homo sapiens (human) ]

Gene ID: 123466219, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123466219
Gene description
Sharpr-MPRA regulatory region 6001
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 Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2537562..2537856)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2536307..2536601)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2539289..2539583)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374353 Neighboring gene uncharacterized LOC107986250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15170 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2470739-2471311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2478879-2479379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2480295-2480819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21176 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2487795-2488296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2491261-2492041 Neighboring gene ring finger protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2556971-2557807 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2557808-2558643 Neighboring gene family with sequence similarity 193 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2561739-2562277 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2597477-2598429 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2598430-2599381 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2599382-2600334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2620021-2620522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2625441-2626235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2632219-2632720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2632721-2633220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2648543-2649043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2660247-2660748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2660749-2661248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2672935-2673479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2746569-2747069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15178 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15179 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2763311-2764135 Neighboring gene uncharacterized LOC102723763 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2764939-2765507 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21183 Neighboring gene TNFAIP3 interacting protein 2

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid silent region 15177

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_077494.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    2537562..2537856
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    2536307..2536601
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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