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LOC130006171 ATAC-STARR-seq lymphoblastoid active region 5076 [ Homo sapiens (human) ]

Gene ID: 130006171, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006171
Gene description
ATAC-STARR-seq lymphoblastoid active region 5076
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 LOC130006171 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 (67267992..67268041)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (67261948..67261997)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67035463..67035512)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902695 Neighboring gene lysine demethylase 2A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66964839-66965339 Neighboring gene small nucleolar RNA U13 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:66989729-66990608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5075 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:67020970-67022169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5077 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5078 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67038522-67039486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67039487-67040451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67044441-67045054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67045055-67045668 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5083 Neighboring gene G protein-coupled receptor kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3621 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67057124-67058048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67058049-67058971 Neighboring gene ankyrin repeat domain 13D Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67070151-67070668 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67070669-67071188 Neighboring gene slingshot protein phosphatase 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_185616.1 

    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
    67267992..67268041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    67261948..67261997
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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