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LOC121587538 Sharpr-MPRA regulatory region 7417 [ Homo sapiens (human) ]

Gene ID: 121587538, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121587538
Gene description
Sharpr-MPRA regulatory region 7417
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 Sharpr-MPRA (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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate 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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See LOC121587538 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (27375048..27375342)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (27653795..27654089)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (27386369..27386663)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NSE1 homolog, SMC5-SMC6 complex component Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7299 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:27282975-27283523 Neighboring gene NSMCE1 divergent transcript Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:27322486-27323685 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:27324508-27325238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10615 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7303 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:27335787-27336641 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:27338789-27339453 Neighboring gene interleukin 4 receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27374892-27375392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27375393-27375893 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:27376379-27377578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10616 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10617 Neighboring gene MPRA-validated peak2541 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10618 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27413572-27414114 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr16:27416784-27417372 and GRCh37_chr16:27417373-27417961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10624 Neighboring gene MPRA-validated peak2542 silencer Neighboring gene interleukin 21 receptor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27449769-27450714 Neighboring gene uncharacterized LOC124903668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27460829-27461706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10631 Neighboring gene IL21R antisense RNA 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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 active region 10619

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_074825.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    27375048..27375342
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    27653795..27654089
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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