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LOC129936336 ATAC-STARR-seq lymphoblastoid active region 19575 [ Homo sapiens (human) ]

Gene ID: 129936336, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936336
Gene description
ATAC-STARR-seq lymphoblastoid active region 19575
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 LOC129936336 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 (19540704..19540813)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (19544754..19544863)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (19582196..19582305)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene potassium voltage-gated channel subfamily H member 8 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:19375136-19375636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14130 Neighboring gene microRNA 4791 Neighboring gene uncharacterized LOC105376982 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:19491994-19493193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19576 Neighboring gene NANOG hESC enhancer GRCh37_chr3:19709582-19710083 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:19713203-19713703 Neighboring gene uncharacterized LOC105376984 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67588 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:19896761-19897348 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:19906013-19907212 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67669 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67675 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67680 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67685 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_67687 and experimental_67689 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67692 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67694 Neighboring gene Sharpr-MPRA regulatory region 12217 Neighboring gene EF-hand domain family member B Neighboring gene heat shock protein family A (Hsp70) member 8 pseudogene 18

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_169347.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    19540704..19540813
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    19544754..19544863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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