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LOC130059440 ATAC-STARR-seq lymphoblastoid silent region 7724 [ Homo sapiens (human) ]

Gene ID: 130059440, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059440
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7724
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 LOC130059440 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 (75555943..75556022)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81604190..81604269)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75589841..75589920)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene TMEM231 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7722 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7723 Neighboring gene carbohydrate sulfotransferase 5 Neighboring gene transmembrane protein 231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11138 Neighboring gene Sharpr-MPRA regulatory region 12601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75600739-75601492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11139 Neighboring gene GABA type A receptor associated protein like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11140 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11142 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75626991-75627988 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75627989-75628985 Neighboring gene adenosine deaminase tRNA specific 1 Neighboring gene Sharpr-MPRA regulatory region 14871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75655412-75655932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75655933-75656452 Neighboring gene H3K27ac hESC enhancers GRCh37_chr16:75656453-75656972 and GRCh37_chr16:75656973-75657492

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_193861.1 

    Range
    101..180
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    75555943..75556022
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    81604190..81604269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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