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LOC129998653 ATAC-STARR-seq lymphoblastoid silent region 18285 [ Homo sapiens (human) ]

Gene ID: 129998653, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129998653
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18285
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 LOC129998653 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 (74657268..74657427)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (75859553..75859712)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (74071595..74071754)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene GTF2I repeat domain containing 1 Neighboring gene Williams-Beuren syndrome chromosome region 23 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73995345-73995846 Neighboring gene Sharpr-MPRA regulatory region 2459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74001529-74002116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74002117-74002703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74031162-74031727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74031728-74032292 Neighboring gene microRNA 10525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26168 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74075507-74076155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26175 Neighboring gene general transcription factor IIi Neighboring gene GTF2I antisense RNA 1 Neighboring gene Williams-Beuren syndrome medial block B recombination region Neighboring gene PHB1 pseudogene 15

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_178099.1 

    Range
    101..260
    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
    74657268..74657427
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    75859553..75859712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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