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LOC130005225 ATAC-STARR-seq lymphoblastoid active region 4366 [ Homo sapiens (human) ]

Gene ID: 130005225, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005225
Gene description
ATAC-STARR-seq lymphoblastoid active region 4366
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 LOC130005225 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 (7516580..7516629)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (7574940..7574989)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (7537811..7537860)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene synaptotagmin 9 Neighboring gene Sharpr-MPRA regulatory region 13298 Neighboring gene NANOG hESC enhancer GRCh37_chr11:7472795-7473306 Neighboring gene SYT9 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:7506414-7506918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4364 Neighboring gene leucine-rich repeat extensin-like protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4369 Neighboring gene MPRA-validated peak1190 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4370 Neighboring gene olfactomedin like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4373 Neighboring gene PPFIA binding protein 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:7584372-7584873 Neighboring gene uncharacterized LOC105376535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:7595102-7595926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:7595927-7596750 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:7599169-7599403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4374 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:7651972-7653171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4375 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:7672104-7673303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3111 Neighboring gene cytochrome b5 reductase 2

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_184670.1 

    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
    7516580..7516629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    7574940..7574989
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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