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LOC130007056 ATAC-STARR-seq lymphoblastoid silent region 4061 [ Homo sapiens (human) ]

Gene ID: 130007056, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007056
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4061
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 LOC130007056 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (128694704..128694923)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (128727905..128728124)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (128564599..128564818)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5728 Neighboring gene CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128480315-128481964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128485091-128485590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128485724-128486224 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:128491606-128492805 Neighboring gene CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128494058-128494944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128523817-128524317 Neighboring gene uncharacterized LOC101929538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4058 Neighboring gene CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128563455-128564187 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4062 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:128570339-128571538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4063 Neighboring gene NANOG hESC enhancer GRCh37_chr11:128585502-128586027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5733 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:128587835-128588354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5734 Neighboring gene Fli-1 proto-oncogene, ETS transcription factor Neighboring gene smooth muscle and endothelial cell enriched migration/differentiation-associated lncRNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128596161-128596660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5738 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:128603944-128604489 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128627636-128628136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128628137-128628637 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128646623-128647228 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:128654003-128654550 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:128654551-128655097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5741 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:128689257-128689763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5743 Neighboring gene uncharacterized LOC107984409 Neighboring gene Sharpr-MPRA regulatory region 11395 Neighboring gene potassium inwardly rectifying channel subfamily J member 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:128740730-128741492 Neighboring gene NANOG hESC enhancer GRCh37_chr11:128741942-128742537 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:128771525-128772283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4065 Neighboring gene KCNJ5 antisense RNA 1 Neighboring gene potassium inwardly rectifying channel subfamily J member 5

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_186500.1 

    Range
    101..320
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    128694704..128694923
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    128727905..128728124
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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