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LOC130066248 ATAC-STARR-seq lymphoblastoid silent region 13067 [ Homo sapiens (human) ]

Gene ID: 130066248, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066248
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13067
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 LOC130066248 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (57710297..57710416)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (59488291..59488410)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56285353..56285472)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56143743-56144243 Neighboring gene Sharpr-MPRA regulatory region 2062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56165049-56165804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13064 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:56172128-56172301 Neighboring gene phosphoenolpyruvate carboxykinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56193035-56193894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18167 Neighboring gene Z-DNA binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56229759-56230358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56230359-56230956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56236773-56237645 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56238905-56239419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56241925-56242541 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56251833-56252416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56253071-56253587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56253588-56254103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56254668-56255192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56255193-56255716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56257022-56257522 Neighboring gene prostate transmembrane protein, androgen induced 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56267863-56268682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56271371-56271903 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:56272784-56273983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56279768-56280362 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:56283453-56284064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56287125-56287736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56290116-56290644 Neighboring gene uncharacterized LOC105372692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56299854-56300354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56300355-56300855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56319851-56320352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56320353-56320852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56322729-56323588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56323589-56324446 Neighboring gene NF-kappaB interacting lncRNA Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56346807-56347450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:56347451-56348092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56358085-56358678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56369354-56369854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56410252-56410913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56410914-56411574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56474981-56475610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56475611-56476238 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:56496341-56496840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:56527975-56528475 Neighboring gene uncharacterized LOC105372693

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_200665.1 

    Range
    101..220
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    57710297..57710416
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    59488291..59488410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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