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LOC129936904 ATAC-STARR-seq lymphoblastoid active region 19969 [ Homo sapiens (human) ]

Gene ID: 129936904, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936904
Gene description
ATAC-STARR-seq lymphoblastoid active region 19969
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 LOC129936904 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (53749273..53749472)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (53782488..53782687)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (53783300..53783499)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 2578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53528087-53528586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53528917-53529702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53529703-53530487 Neighboring gene ribosomal protein S25 pseudogene 4 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53545870-53546371 Neighboring gene calcium voltage-gated channel subunit alpha1 D Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:53559857-53561056 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53565752-53566253 Neighboring gene NANOG hESC enhancer GRCh37_chr3:53579614-53580115 Neighboring gene uncharacterized LOC124906242 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:53750142-53751341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53752305-53752885 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53752886-53753466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53765682-53766222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53766223-53766761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53787515-53788014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53798133-53798649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53802933-53803434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:53838519-53839320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53840931-53841432 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53841433-53841932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53857324-53857923 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:53878721-53879561 Neighboring gene Sharpr-MPRA regulatory region 239 Neighboring gene choline dehydrogenase Neighboring gene interleukin 17 receptor B Neighboring gene actin related protein 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_169915.1 

    Range
    101..300
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    53749273..53749472
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    53782488..53782687
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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