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LOC129936717 ATAC-STARR-seq lymphoblastoid active region 19841 [ Homo sapiens (human) ]

Gene ID: 129936717, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936717
Gene description
ATAC-STARR-seq lymphoblastoid active region 19841
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 LOC129936717 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 (48663852..48664211)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (48692812..48693171)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (48701285..48701644)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 26 member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14335 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14336 Neighboring gene microRNA 6824 Neighboring gene cadherin EGF LAG seven-pass G-type receptor 3 Neighboring gene microRNA 4793 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48693647-48694344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48694345-48695040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48698042-48698628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48698629-48699213 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48700385-48700970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48702141-48702725 Neighboring gene long intergenic non-protein coding RNA 2585 Neighboring gene NCK interacting protein with SH3 domain Neighboring gene Sharpr-MPRA regulatory region 90 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48725238-48725738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48725739-48726239 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:48732697-48733286 Neighboring gene inositol hexakisphosphate kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:48750133-48750632

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_169728.1 

    Range
    101..460
    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
    48663852..48664211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    48692812..48693171
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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