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LOC130007807 ATAC-STARR-seq lymphoblastoid silent region 4416 [ Homo sapiens (human) ]

Gene ID: 130007807, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007807
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4416
Gene type
biological region
Feature type(s)
regulatory: silencer
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 a silencer based on its ability to repress 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 LOC130007807 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (48969959..48970038)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (48932160..48932239)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (49363742..49363821)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene FKBP prolyl isomerase 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4415 Neighboring gene ARF GTPase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49338542-49339042 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:49340991-49341204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49341223-49341815 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49349467-49350462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6297 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:49353706-49353915 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:49358123-49358716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49360112-49360664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49361393-49362276 Neighboring gene Wnt family member 10B Neighboring gene Sharpr-MPRA regulatory region 4091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4417 Neighboring gene RNA, U6 small nuclear 940, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49373043-49373642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49373643-49374244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6298 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49374845-49375445 Neighboring gene uncharacterized LOC105369757 Neighboring gene Wnt family member 1

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_188396.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    48969959..48970038
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    48932160..48932239
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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