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LOC130059377 ATAC-STARR-seq lymphoblastoid silent region 7689 [ Homo sapiens (human) ]

Gene ID: 130059377, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130059377
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7689
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 LOC130059377 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 (72847314..72847373)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (78665126..78665185)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (72881213..72881272)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ZFHX3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:72769685-72770266 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44255 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:72804631-72805830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:72822417-72823032 Neighboring gene keratin 18 pseudogene 18 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72879311-72879810 Neighboring gene uncharacterized LOC124903715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72912157-72912658 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:72910943-72912142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72923795-72924295 Neighboring gene RNA, U7 small nuclear 71 pseudogene Neighboring gene zinc finger homeobox 3 Neighboring gene Sharpr-MPRA regulatory region 11593 Neighboring gene Sharpr-MPRA regulatory region 14271 Neighboring gene VISTA enhancer hs16 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:72995175-72995675 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:73049174-73049674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11101 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73066446-73067008 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73069350-73070204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:73070205-73071057 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr16:73074111-73074623 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73078457-73078957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73081321-73081856 Neighboring gene uncharacterized LOC124903719 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:73082393-73082928

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_193798.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    72847314..72847373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    78665126..78665185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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