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LOC130005908 ATAC-STARR-seq lymphoblastoid active region 4883 [ Homo sapiens (human) ]

Gene ID: 130005908, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005908
Gene description
ATAC-STARR-seq lymphoblastoid active region 4883
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 LOC130005908 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 (64185294..64185363)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64175239..64175308)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (63952766..63952835)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene mono-ADP ribosylhydrolase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63803443-63804345 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63804346-63805247 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63815687-63816245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63816558-63817058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63820013-63820556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63820557-63821100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63821645-63822187 Neighboring gene fibronectin leucine rich transmembrane protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63826482-63827200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63836633-63837360 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:63840775-63840963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63860723-63861393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63861723-63862230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63877842-63878622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63889359-63890290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63896949-63897542 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63913439-63913940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63919856-63920851 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63920852-63921846 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:63933104-63933604 Neighboring gene uncharacterized LOC105369339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3460 Neighboring gene MPRA-validated peak1294 silencer Neighboring gene uncharacterized LOC124902686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63948751-63949252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63949253-63949752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63951637-63952142 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3462 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr11:63972802-63973364 and GRCh37_chr11:63973365-63973927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4886 Neighboring gene stress induced phosphoprotein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4889 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:63992564-63993286 Neighboring gene FERM domain containing kindlin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63993887-63994406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:63994407-63994924 Neighboring gene uncharacterized LOC124902687 Neighboring gene nudix hydrolase 22 Neighboring gene tRNA phosphotransferase 1

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_185353.1 

    Range
    101..170
    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
    64185294..64185363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    64175239..64175308
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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