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LOC129937063 ATAC-STARR-seq lymphoblastoid silent region 14534 [ Homo sapiens (human) ]

Gene ID: 129937063, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129937063
Gene description
ATAC-STARR-seq lymphoblastoid silent region 14534
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 represents an accessible chromatin region 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) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129937063 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (72996666..72997295)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (73038566..73039195)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (73045817..73046446)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14532 Neighboring gene lysosomal protein transmembrane 4 beta pseudogene 2 Neighboring gene glucoside xylosyltransferase 2 Neighboring gene ferritin heavy chain 1 pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20094 Neighboring gene Sharpr-MPRA regulatory region 10271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20095 Neighboring gene uncharacterized LOC124909395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20097 Neighboring gene protein phosphatase 4 regulatory subunit 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:73077426-73077926 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:73077927-73078427 Neighboring gene RNA, U7 small nuclear 19 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:73097059-73097560 Neighboring gene Sharpr-MPRA regulatory region 10785 Neighboring gene MPRA-validated peak4698 silencer Neighboring gene endogenous Bornavirus like nucleoprotein 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. 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)

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_170073.1 

    Range
    101..730
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    72996666..72997295
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    73038566..73039195
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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