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LOC130056685 ATAC-STARR-seq lymphoblastoid silent region 6236 [ Homo sapiens (human) ]

Gene ID: 130056685, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056685
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6236
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 LOC130056685 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (105419521..105419570)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99667050..99667099)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (105885858..105885907)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene phosphofurin acidic cluster sorting protein 2 Neighboring gene ribosomal protein S20 pseudogene 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105856860-105857360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105857361-105857861 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105864965-105865475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105865476-105865986 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6232 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105877939-105878442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105878443-105878945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6234 Neighboring gene testis expressed 22 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105884361-105885030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105887709-105888376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105888377-105889046 Neighboring gene MTA1 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105903142-105903739 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105903740-105904336 Neighboring gene metastasis associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105930591-105931113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105931114-105931635 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105937181-105938044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105939600-105940132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6243 Neighboring gene cysteine rich protein 2

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_191106.1 

    Range
    101..150
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    105419521..105419570
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    99667050..99667099
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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