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LOC121852969 Sharpr-MPRA regulatory region 3490 [ Homo sapiens (human) ]

Gene ID: 121852969, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121852969
Gene description
Sharpr-MPRA regulatory region 3490
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. A subregion 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 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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Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (62586125..62586470)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (62789000..62789345)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (60253409..60253703)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9507 Neighboring gene ribosomal protein L17 pseudogene 44 Neighboring gene ACTB pseudogene 9 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_49001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13431 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_49008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:60190967-60191540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9514 Neighboring gene zinc finger CCHC-type containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:60278845-60279519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13434 Neighboring gene RNA, 7SL, cytoplasmic 705, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_49084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9516 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:60383195-60384157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9520 Neighboring gene RNA, U6 small nuclear 142, pseudogene Neighboring gene PH domain and leucine rich repeat protein phosphatase 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 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 active region 13433

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_076076.2 

    Range
    101..446
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    62586125..62586470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    62789000..62789345
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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