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LOC130008067 ATAC-STARR-seq lymphoblastoid silent region 4553 [ Homo sapiens (human) ]

Gene ID: 130008067, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008067
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4553
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 LOC130008067 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (56258023..56258572)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (56225653..56226202)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (56651807..56652356)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56615664-56616598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56616599-56617532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4551 Neighboring gene nucleic acid binding protein 2 Neighboring gene solute carrier family 39 member 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:56630689-56630907 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29670 Neighboring gene ankyrin repeat domain 52 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29671 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:56650178-56651170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4554 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29674 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6485 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:56660797-56661296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6486 Neighboring gene Sharpr-MPRA regulatory region 15563 Neighboring gene coenzyme Q10A Neighboring gene citrate synthase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_29678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:56693295-56693812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4556 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4557

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_188603.1 

    Range
    101..650
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    56258023..56258572
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    56225653..56226202
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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