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LOC130006309 ATAC-STARR-seq lymphoblastoid active region 5167 [ Homo sapiens (human) ]

Gene ID: 130006309, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006309
Gene description
ATAC-STARR-seq lymphoblastoid active region 5167
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 LOC130006309 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 (71452042..71452121)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (71378997..71379076)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (71163088..71163167)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene actin epsilon 1, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3707 Neighboring gene 7-dehydrocholesterol reductase Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:71159471-71159972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71164405-71164906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71164907-71165406 Neighboring gene DHCR7 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr11:71169226-71169406 Neighboring gene NAD synthetase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71183373-71184280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71184281-71185187 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71187723-71188302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71188303-71188882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71188883-71189462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:71191463-71191988 Neighboring gene microRNA 6754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71196200-71196700 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:71198988-71199758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:71211789-71212476 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:71216417-71217007 Neighboring gene S100A11 pseudogene 3

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_185754.1 

    Range
    101..180
    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
    71452042..71452121
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    71378997..71379076
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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