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LOC130007178 ATAC-STARR-seq lymphoblastoid silent region 4127 [ Homo sapiens (human) ]

Gene ID: 130007178, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130007178
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4127
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: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (2034942..2035231)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (2031068..2031357)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:2063223-2064422 Neighboring gene Sharpr-MPRA regulatory region 10568 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:2112705-2113344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5813 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:2120775-2121283 Neighboring gene decapping mRNA 1B Neighboring gene calcium voltage-gated channel subunit alpha1 C Neighboring gene CACNA1C intronic transcript 1 Neighboring gene NANOG hESC enhancer GRCh37_chr12:2158750-2159251 Neighboring gene CACNA1C intronic transcript 2 Neighboring gene uncharacterized LOC107984131 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2244697-2245492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:2246289-2247084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2248447-2248948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:2248949-2249448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4128

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_187852.1 

    Range
    101..390
    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
    2034942..2035231
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654718.1 Reference GRCh38.p14 PATCHES

    Range
    377086..377375
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    2031068..2031357
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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