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LOC130007014 ATAC-STARR-seq lymphoblastoid active region 5698 [ Homo sapiens (human) ]

Gene ID: 130007014, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007014
Gene description
ATAC-STARR-seq lymphoblastoid active region 5698
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 LOC130007014 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 (125570145..125570194)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (125598793..125598842)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (125440041..125440090)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene PBX/knotted 1 homeobox 2 Neighboring gene RNA, U6 small nuclear 321, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125181994-125182578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125211245-125211994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125219321-125219863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:125220519-125221182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:125221183-125221844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125239164-125240045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125241808-125242687 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:125278650-125279849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125296399-125296900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125298605-125299508 Neighboring gene Sharpr-MPRA regulatory region 8813 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:125314964-125315827 Neighboring gene Sharpr-MPRA regulatory region 13231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5697 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:125364213-125364716 Neighboring gene fasciculation and elongation protein zeta 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125365219-125365722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:125365723-125366224 Neighboring gene putative uncharacterized protein MGC39545 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5907 Neighboring gene Sharpr-MPRA regulatory region 4861 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5909 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5910 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:125439037-125439538 Neighboring gene STT3A antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1156, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5699 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:125462019-125462613 Neighboring gene EI24 autophagy associated transmembrane protein Neighboring gene STT3 oligosaccharyltransferase complex catalytic subunit A

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_186458.1 

    Range
    101..150
    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
    125570145..125570194
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    125598793..125598842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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