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LOC130001254 ATAC-STARR-seq lymphoblastoid silent region 19574 [ Homo sapiens (human) ]

Gene ID: 130001254, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001254
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19574
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 LOC130001254 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 (140358782..140358841)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (141478966..141479025)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (141368881..141368940)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene trafficking protein particle complex subunit 9 Neighboring gene uncharacterized LOC124902029 Neighboring gene MPRA-validated peak7188 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:141274731-141275554 Neighboring gene uncharacterized LOC105375779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141282982-141283482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141309152-141309652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141309653-141310153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141312322-141312822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141312823-141313323 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr8:141319328-141320527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141320544-141321044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141321045-141321545 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:141341524-141342398 Neighboring gene Sharpr-MPRA regulatory region 993 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:141355797-141356018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141375096-141375596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:141375597-141376097 Neighboring gene Sharpr-MPRA regulatory region 8823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:141458229-141458802 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:141458803-141459375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19576 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:141468097-141468615 Neighboring gene uncharacterized LOC105375782 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:141474198-141475397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19579 Neighboring gene MPRA-validated peak7190 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr8:141518766-141518946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28029 Neighboring gene chromatin accessibility complex subunit 1

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_180700.1 

    Range
    101..160
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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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    140358782..140358841
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    141478966..141479025
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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