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LOC130056556 ATAC-STARR-seq lymphoblastoid silent region 6137 [ Homo sapiens (human) ]

Gene ID: 130056556, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056556
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6137
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 LOC130056556 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (103044254..103044303)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (97280505..97280554)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (103510591..103510640)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6134 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103390587-103390785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6136 Neighboring gene CDC42 binding protein kinase beta Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:103411482-103412681 Neighboring gene amnion associated transmembrane protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103452779-103453413 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103453414-103454047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103464738-103465284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9093 Neighboring gene Sharpr-MPRA regulatory region 6354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103486267-103486822 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103489632-103489899 Neighboring gene Sharpr-MPRA regulatory region 14595 Neighboring gene ribosomal protein L13 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103524373-103525023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103541151-103541742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103559931-103560500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:103561071-103561640 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:103564684-103564853 Neighboring gene LBH domain containing 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103570895-103571645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103576032-103576642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:103576643-103577253 Neighboring gene exocyst complex component 3 like 4

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_190977.1 

    Range
    101..150
    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
    103044254..103044303
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    97280505..97280554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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