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LOC129999788 ATAC-STARR-seq lymphoblastoid silent region 18883 [ Homo sapiens (human) ]

Gene ID: 129999788, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999788
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18883
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 LOC129999788 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 (6708396..6708735)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (6463793..6464132)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (6565917..6566256)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene microcephalin 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:6385720-6386919 Neighboring gene angiopoietin 2 Neighboring gene Sharpr-MPRA regulatory region 12768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:6419583-6420108 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6420109-6420635 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6434138-6434684 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:6436241-6436413 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_103492 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:6446215-6446714 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6450530-6451446 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:6451447-6452362 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:6456108-6457307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:6459927-6460426 Neighboring gene NANOG hESC enhancer GRCh37_chr8:6473596-6474097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:6481178-6481678 Neighboring gene MCPH1 antisense RNA 1 Neighboring gene microRNA 8055 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:6505663-6506862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26951 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18884 Neighboring gene protein tyrosine phosphatase non-receptor type 4 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26953 Neighboring gene 1-acylglycerol-3-phosphate O-acyltransferase 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26955 Neighboring gene microRNA 4659a Neighboring gene microRNA 4659b

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_179234.1 

    Range
    101..440
    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
    6708396..6708735
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    103666..104005
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    6463793..6464132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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