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LOC130004129 ATAC-STARR-seq lymphoblastoid active region 3606 [ Homo sapiens (human) ]

Gene ID: 130004129, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004129
Gene description
ATAC-STARR-seq lymphoblastoid active region 3606
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 LOC130004129 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (75044176..75044285)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (75917706..75917815)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (76803934..76804043)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3598 Neighboring gene uncharacterized LOC124902459 Neighboring gene VISTA enhancer hs1500 Neighboring gene MPRA-validated peak1017 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:76555535-76556121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:76584665-76585436 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:76585437-76586208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2504 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:76615828-76616038 Neighboring gene lysine acetyltransferase 6B Neighboring gene ReSE screen-validated silencer GRCh37_chr10:76630209-76630443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3601 Neighboring gene MPRA-validated peak1019 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3602 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:76776654-76776821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76789883-76790382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3605 Neighboring gene small nucleolar RNA, C/D box 172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76817979-76818530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76829139-76829638 Neighboring gene dual specificity phosphatase 29 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:76836023-76836606 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:76839714-76840274 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:76839152-76839713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76842102-76842602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76844610-76845110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:76863200-76864044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:76864045-76864889 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:76865735-76866578 Neighboring gene peptidylprolyl isomerase A pseudogene 13 Neighboring gene dual specificity phosphatase 13B Neighboring gene dual specificity phosphatase 13A Neighboring gene sterile alpha motif domain containing 8

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_183575.1 

    Range
    101..210
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    75044176..75044285
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646202.1 Reference GRCh38.p14 PATCHES

    Range
    248852..248961
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    75917706..75917815
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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