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LOC129934067 ATAC-STARR-seq lymphoblastoid active region 16019 [ Homo sapiens (human) ]

Gene ID: 129934067, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129934067
Gene description
ATAC-STARR-seq lymphoblastoid active region 16019
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 LOC129934067 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (71545747..71545826)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (71556833..71556912)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (71772877..71772956)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374797 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:71558505-71559192 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:71559193-71559878 Neighboring gene Sharpr-MPRA regulatory region 7735 Neighboring gene zinc finger protein 638 Neighboring gene RNA, U6 small nuclear 105, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71643743-71644372 Neighboring gene Sharpr-MPRA regulatory region 6666 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:71672359-71672860 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:71678052-71678238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71680549-71681398 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71681399-71682247 Neighboring gene VISTA enhancer hs2170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71727399-71728077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71730437-71730936 Neighboring gene Sharpr-MPRA regulatory region 7639 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:71733683-71734184 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:71734185-71734684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71739143-71739642 Neighboring gene NANOG hESC enhancer GRCh37_chr2:71754884-71755402 Neighboring gene dysferlin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71780379-71780878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71779877-71780378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71787253-71787780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71813506-71814014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71814015-71814523 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71815560-71816140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71821207-71821706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71825151-71825652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:71825653-71826152 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:71829831-71831030 Neighboring gene VISTA enhancer hs1479 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71920591-71921090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:71921091-71922090 Neighboring gene uncharacterized LOC124907827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72018477-72019464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72021448-72022059 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:72057331-72058530 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:72070213-72070395 Neighboring gene Sharpr-MPRA regulatory region 1897 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:72107588-72108787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72120471-72120972 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72120973-72121472 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:72124986-72125167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72157000-72157500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:72159067-72159946 Neighboring gene ribosomal protein S20 pseudogene 10

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_167091.1 

    Range
    101..180
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    71545747..71545826
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    71556833..71556912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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