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LOC129936705 ATAC-STARR-seq lymphoblastoid active region 19831 [ Homo sapiens (human) ]

Gene ID: 129936705, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936705
Gene description
ATAC-STARR-seq lymphoblastoid active region 19831
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 LOC129936705 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 (48469921..48470070)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (48497926..48498075)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48511320..48511469)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14330 Neighboring gene coiled-coil domain containing 51 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14331 Neighboring gene ATRIP-TREX1 readthrough Neighboring gene translation machinery associated 7 homolog Neighboring gene ATR interacting protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19829 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48507557-48508438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48508439-48509318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48509460-48510226 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48513959-48514818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19833 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48515680-48516539 Neighboring gene three prime repair exonuclease 1 Neighboring gene shisa family member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14333 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48542139-48542692 Neighboring gene MPRA-validated peak4641 silencer Neighboring gene 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:48587865-48588528 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:48588529-48589190 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48589191-48589854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48589855-48590516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19836 Neighboring gene microRNA 6823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48596699-48597640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19837 Neighboring gene urocortin 2

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_169716.1 

    Range
    101..250
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    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
    48469921..48470070
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    48497926..48498075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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