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LOC129999810 ATAC-STARR-seq lymphoblastoid silent region 18893 [ Homo sapiens (human) ]

Gene ID: 129999810, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999810
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18893
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 LOC129999810 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (8284160..8284229)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (11459403..11459472, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (8141682..8141751)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 85 member B Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:8024368-8025196 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8025197-8026026 Neighboring gene ectonucleotide pyrophosphatase/phosphodiesterase 7 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:8032372-8033096 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:8038385-8038619 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:8039463-8040118 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8040119-8040774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8051667-8052173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:8052174-8052679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26962 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8090135-8091040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8093271-8093782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8094893-8095443 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8094341-8094892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26963 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:8101423-8102622 Neighboring gene family with sequence similarity 86, member A pseudogene Neighboring gene ALG1 like 13, pseudogene Neighboring gene Sharpr-MPRA regulatory region 6714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8145864-8146364 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:8153089-8154288 Neighboring gene uncharacterized LOC124901879 Neighboring gene PEAK1 related, kinase-activating pseudokinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26966 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:8219633-8220832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8233601-8234540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8238570-8239092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:8239093-8239613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18895 Neighboring gene uncharacterized LOC105379222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:8256091-8256704

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 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_179256.1 

    Range
    101..170
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    8284160..8284229
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    5063623..5063692 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    11459403..11459472 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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