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LOC129999630 ATAC-STARR-seq lymphoblastoid silent region 18802 [ Homo sapiens (human) ]

Gene ID: 129999630, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999630
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18802
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 LOC129999630 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 (151115523..151115582)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (152288610..152288669)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150812610..150812669)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:150777216-150778191 Neighboring gene Sharpr-MPRA regulatory region 12172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18797 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18799 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26851 Neighboring gene uncharacterized LOC124901778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150786615-150787125 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150787126-150787635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150787761-150788266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150788267-150788772 Neighboring gene transmembrane and ubiquitin like domain containing 1 Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:150800613-150801520 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:150805265-150805927 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150828941-150829442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150829443-150829942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150833002-150833976 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:150834950-150835923 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:150835924-150836896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150840191-150841150 Neighboring gene gastrulation brain homeobox 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18804 Neighboring gene Sharpr-MPRA regulatory region 15220 Neighboring gene MPRA-validated peak6845 silencer Neighboring gene ankyrin repeat and SOCS box containing 10

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_179076.1 

    Range
    101..160
    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
    151115523..151115582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    152288610..152288669
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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