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LOC130006035 ATAC-STARR-seq lymphoblastoid active region 4988 [ Homo sapiens (human) ]

Gene ID: 130006035, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006035
Gene description
ATAC-STARR-seq lymphoblastoid active region 4988
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 LOC130006035 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 (65569835..65570554)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65564067..65564786)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65337306..65338025)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3529 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65297753-65297921 Neighboring gene SCY1 like pseudokinase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305475-65305979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305980-65306483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3530 Neighboring gene Sharpr-MPRA regulatory region 4001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4987 Neighboring gene latent transforming growth factor beta binding protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3535 Neighboring gene uncharacterized LOC124902823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65319617-65320292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65320293-65320968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65328600-65329263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4989 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3539 Neighboring gene ZNRD2 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3541 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3543 Neighboring gene zinc ribbon domain containing 2 Neighboring gene Sharpr-MPRA regulatory region 14514 Neighboring gene family with sequence similarity 89 member B Neighboring gene uncharacterized LOC124902692 Neighboring gene EH domain binding protein 1 like 1

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_185480.1 

    Range
    101..820
    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
    65569835..65570554
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65564067..65564786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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