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LOC129999544 ATAC-STARR-seq lymphoblastoid silent region 18747 [ Homo sapiens (human) ]

Gene ID: 129999544, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999544
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18747
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 LOC129999544 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 (149126654..149127093)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (150308457..150308896)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (148823746..148824185)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148768421-148769413 Neighboring gene zinc finger protein 786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18746 Neighboring gene MPRA-validated peak6836 silencer Neighboring gene MPRA-validated peak6837 silencer Neighboring gene zinc finger protein 425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:148821330-148821830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:148821831-148822331 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148822579-148823130 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148823131-148823682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26808 Neighboring gene RNA, 7SL, cytoplasmic 521, pseudogene Neighboring gene zinc finger protein 398 Neighboring gene uncharacterized LOC107986856 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:148842175-148842748 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148842749-148843322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148843323-148843896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26809 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:148844471-148845044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148853225-148853792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148853793-148854358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:148854359-148854926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26811 Neighboring gene centrosomal protein 83kDa pseudogene

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_178990.1 

    Range
    101..540
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    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
    149126654..149127093
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    150308457..150308896
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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