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LOC130005273 ATAC-STARR-seq lymphoblastoid active region 4408 [ Homo sapiens (human) ]

Gene ID: 130005273, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005273
Gene description
ATAC-STARR-seq lymphoblastoid active region 4408
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 LOC130005273 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 (9460546..9460625)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (9545675..9545754)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (9482093..9482172)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 41B Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9335331-9335848 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:9335849-9336364 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9339994-9340970 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:9340971-9341947 Neighboring gene proline rich 13 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9372391-9372892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:9376493-9376993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9377088-9377646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9377647-9378203 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:9385258-9386457 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9406201-9406716 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:9420900-9421065 Neighboring gene importin 7 Neighboring gene Sharpr-MPRA regulatory region 11606 Neighboring gene small nucleolar RNA, H/ACA box 23 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9480928-9481563 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3126 Neighboring gene ZNF143 antisense RNA 1 Neighboring gene zinc finger protein 143 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3127 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9537259-9537799 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9551203-9551929 Neighboring gene CRISPRi-validated cis-regulatory element chr11.1006 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:9584901-9585400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4409 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3128 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:9594443-9595295 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3131 Neighboring gene small nucleolar RNA U13 Neighboring gene WEE1 G2 checkpoint kinase

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_184718.1 

    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
    9460546..9460625
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    9545675..9545754
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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