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LOC129999299 ATAC-STARR-seq lymphoblastoid silent region 18624 [ Homo sapiens (human) ]

Gene ID: 129999299, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999299
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18624
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 LOC129999299 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (129169187..129169406)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (130482092..130482311)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (128809028..128809247)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:128767334-128767834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26623 Neighboring gene mitogen-activated protein kinase kinase 2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:128789516-128790112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:128790113-128790709 Neighboring gene tetraspanin 33 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26625 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:128809737-128810606 Neighboring gene RNY1 pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18625 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18626 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:128856579-128857167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26627 Neighboring gene Sharpr-MPRA regulatory region 13971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18628 Neighboring gene smoothened, frizzled class receptor Neighboring gene adenosylhomocysteinase like 2 Neighboring gene Sharpr-MPRA regulatory region 5606 Neighboring gene uncharacterized LOC124900234 Neighboring gene MPRA-validated peak6717 silencer

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_178745.1 

    Range
    101..320
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    129169187..129169406
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    130482092..130482311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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