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LOC130005940 ATAC-STARR-seq lymphoblastoid active region 4905 [ Homo sapiens (human) ]

Gene ID: 130005940, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005940
Gene description
ATAC-STARR-seq lymphoblastoid active region 4905
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 LOC130005940 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 (64625169..64625218)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (64618150..64618199)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64392641..64392690)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64325867-64326380 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64327331-64327499 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64332286-64333255 Neighboring gene solute carrier family 22 member 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64338776-64339380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64350049-64350932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64350933-64351815 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64352037-64352222 Neighboring gene solute carrier family 22 member 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64372269-64373070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64387298-64387914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64387915-64388530 Neighboring gene neurexin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64404690-64405258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64414407-64414908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64414909-64415408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64415526-64416494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64419195-64419694 Neighboring gene NRXN2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64421037-64421537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64424149-64424650 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64424651-64425150 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:64426961-64428160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64455312-64456232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4907 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64480596-64481379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3481 Neighboring gene Sharpr-MPRA regulatory region 4107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64492769-64493607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64506559-64507108 Neighboring gene RAS guanyl releasing protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3486

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 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_185385.1 

    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
    64625169..64625218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    64618150..64618199
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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