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LOC130058203 ATAC-STARR-seq lymphoblastoid silent region 7014 [ Homo sapiens (human) ]

Gene ID: 130058203, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058203
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7014
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 LOC130058203 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (1983945..1984484)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (2003890..2004429)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2033946..2034485)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ring finger protein 151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10249 Neighboring gene transducin beta like 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2028013-2028592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2028593-2029172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2029173-2029752 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr16:2029753-2030330 and GRCh37_chr16:2030331-2030910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10250 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:2032733-2032925 Neighboring gene NADPH oxidase organizer 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2038929-2039508 Neighboring gene growth factor, augmenter of liver regeneration Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2041827-2042404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2042985-2043562 Neighboring gene synaptogyrin 3 Neighboring gene zinc finger protein 598, E3 ubiquitin ligase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7019 Neighboring gene Sharpr-MPRA regulatory region 7653 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2056701-2057648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2059548-2060496

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_192624.1 

    Range
    101..640
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    1983945..1984484
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791799.1 Reference GRCh38.p14 PATCHES

    Range
    50093..50632
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    2003890..2004429
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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