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LOC130006256 ATAC-STARR-seq lymphoblastoid active region 5140 [ Homo sapiens (human) ]

Gene ID: 130006256, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006256
Gene description
ATAC-STARR-seq lymphoblastoid active region 5140
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC130006256 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 (68460423..68460482)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (68465327..68465386)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (68227891..68227950)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68080045-68080920 Neighboring gene uncharacterized LOC124900302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68080921-68081795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68082507-68083006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68084075-68084742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68095823-68096400 Neighboring gene uncharacterized LOC124902698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68099859-68100434 Neighboring gene LDL receptor related protein 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68110204-68111055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68120602-68121235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68121869-68122501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68141212-68141935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5138 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:68154179-68154402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68164501-68165000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3671 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:68185667-68186590 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68213843-68214446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68214447-68215051 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68215052-68215655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3673 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68237400-68237900 Neighboring gene protein phosphatase 6 regulatory subunit 3 Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68278329-68278907 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68278908-68279485 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:68307752-68308457 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68310718-68311218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68311219-68311719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68351250-68351750 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:68370649-68370853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68376961-68377462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68377463-68377962 Neighboring gene NANOG hESC enhancer GRCh37_chr11:68390073-68390603 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:68399697-68400286 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:68400287-68400875 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:68400876-68401464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68419596-68420268 Neighboring gene uncharacterized LOC107984343 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68450731-68451406 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68452083-68452758 Neighboring gene galanin and GMAP prepropeptide

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 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_185701.1 

    Range
    101..160
    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
    68460423..68460482
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    68465327..68465386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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