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LOC130006922 ATAC-STARR-seq lymphoblastoid active region 5639 [ Homo sapiens (human) ]

Gene ID: 130006922, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006922
Gene description
ATAC-STARR-seq lymphoblastoid active region 5639
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 LOC130006922 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 (120613023..120613362)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (120636041..120636380)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (120483732..120484071)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3991 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:120224214-120224428 Neighboring gene Rho guanine nucleotide exchange factor 12 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120249395 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120288060 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120305787 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120306759 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120313899 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120345004 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120350393 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 11:120356317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3993 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120386966-120387568 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120387569-120388170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120402421-120402957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120418648-120419393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120435257-120435837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120435838-120436417 Neighboring gene glutamate ionotropic receptor kainate type subunit 4 Neighboring gene uncharacterized LOC107984400 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:120479691-120480414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120480713-120481226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120498105-120498605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120504647-120505626 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:120515748-120516454 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:120516455-120517161 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120530966-120531466 Neighboring gene elongin C pseudogene 22 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120537690-120538200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:120538201-120538710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120551815-120552316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120566465-120566964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120581457-120582198 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:120630117-120630617 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:120642173-120642737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120646481-120647262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120647263-120648044 Neighboring gene NANOG hESC enhancer GRCh37_chr11:120662921-120663458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120667409-120667910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:120667911-120668410 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:120669439-120670113 Neighboring gene uncharacterized LOC105369532

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_186366.1 

    Range
    101..440
    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
    120613023..120613362
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    120636041..120636380
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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