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LOC130066457 ATAC-STARR-seq lymphoblastoid silent region 13217 [ Homo sapiens (human) ]

Gene ID: 130066457, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066457
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13217
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 LOC130066457 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (15065342..15065521)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (13420525..13420704)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (16437663..16437842)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61623 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18283 Neighboring gene adipocyte associated metabolic related lncRNA 1 Neighboring gene RBMX2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18286 Neighboring gene Sharpr-MPRA regulatory region 6418 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:16267450-16268649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18287 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:16283327-16284086 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:16284087-16284844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:16299057-16299650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:16299651-16300242 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61697 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61707 Neighboring gene nuclear receptor interacting protein 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16377340-16378275 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61740 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:16403577-16404776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18292 Neighboring gene long intergenic non-protein coding RNA 2920 Neighboring gene uncharacterized LOC107985483 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:16493536-16494052 Neighboring gene Sharpr-MPRA regulatory region 10595

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_200874.1 

    Range
    101..280
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    15065342..15065521
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    13420525..13420704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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