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LOC129936320 ATAC-STARR-seq lymphoblastoid active region 19562 [ Homo sapiens (human) ]

Gene ID: 129936320, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936320
Gene description
ATAC-STARR-seq lymphoblastoid active region 19562
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 LOC129936320 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 (17054420..17054609)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (17056457..17056646)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (17095912..17096101)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16924592-16925300 Neighboring gene uncharacterized LOC105376972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16926303-16926804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16926805-16927304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19557 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19559 Neighboring gene phospholipase C like 2 Neighboring gene microRNA 3714 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:17041383-17041908 Neighboring gene Sharpr-MPRA regulatory region 1410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19561 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:17080505-17081704 Neighboring gene PLCL2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19563 Neighboring gene Sharpr-MPRA regulatory region 1226 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_66731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:17192997-17193498 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:17194853-17195024 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:17199910-17200410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:17200411-17200911 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:17211116-17211616 Neighboring gene NANOG hESC enhancer GRCh37_chr3:17217563-17218064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19568 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14124 Neighboring gene TBC1 domain family member 5 Neighboring gene Sharpr-MPRA regulatory region 10783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19570 Neighboring gene MPRA-validated peak4551 silencer Neighboring gene RBIS pseudogene 6 Neighboring gene Sharpr-MPRA regulatory region 9690 Neighboring gene ribosomal protein L31 pseudogene 19

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_169331.1 

    Range
    101..290
    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
    17054420..17054609
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_017363813.1 Reference GRCh38.p14 PATCHES

    Range
    366888..367077
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    17056457..17056646
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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