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LOC130056580 ATAC-STARR-seq lymphoblastoid silent region 6155 [ Homo sapiens (human) ]

Gene ID: 130056580, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130056580
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6155
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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Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (103521449..103521518)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (97757493..97757562)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene microtubule affinity regulating kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9103 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9104 Neighboring gene ribosomal protein L10a pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103921390-103921890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103921891-103922391 Neighboring gene uncharacterized LOC112268130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103984081-103984968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103986745-103987632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103989409-103990294 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103999205-103999704 Neighboring gene uncharacterized LOC124903392 Neighboring gene creatine kinase B Neighboring gene tRNA methyltransferase 61A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:104008443-104009162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:104009885-104010606 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6159 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9105 Neighboring gene RNA, U7 small nuclear 160 pseudogene

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

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_191001.1 

    Range
    101..170
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    103521449..103521518
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    97757493..97757562
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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