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LOC130009228 ATAC-STARR-seq lymphoblastoid silent region 5098 [ Homo sapiens (human) ]

Gene ID: 130009228, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009228
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5098
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 LOC130009228 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 (131682281..131682430)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (131726098..131726247)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (132166826..132166975)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132156613-132157112 Neighboring gene ribosomal protein S6 pseudogene 21 Neighboring gene uncharacterized LOC105370087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7369 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:132204952-132206151 Neighboring gene splicing factor SWAP Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132213273-132213837 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132216488-132217157 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:132217158-132217826 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:132221080-132222279 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132257981-132258606 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132258607-132259231 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:132269252-132270451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:132271907-132272407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132280316-132281138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132281963-132282784 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:132284875-132285724 Neighboring gene RNA, 5S ribosomal pseudogene 378

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_188872.1 

    Range
    101..250
    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
    131682281..131682430
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    131726098..131726247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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