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LOC130060796 ATAC-STARR-seq lymphoblastoid silent region 8472 [ Homo sapiens (human) ]

Gene ID: 130060796, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130060796
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8472
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 LOC130060796 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (40063008..40063167)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40926893..40927052)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38219261..38219420)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38182900-38183810 Neighboring gene mediator complex subunit 24 Neighboring gene small nucleolar RNA, C/D box 124 Neighboring gene microRNA 6884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38191855-38192722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38216829-38217416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38217417-38218004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38218005-38218590 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38227151-38227756 Neighboring gene thyroid hormone receptor alpha Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38231037-38231892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12123 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38246843-38247468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38247469-38248095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12125 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12126 Neighboring gene Sharpr-MPRA regulatory region 6187 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:38254986-38256185 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12128 Neighboring gene nuclear receptor subfamily 1 group D member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38259215-38260094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38262999-38263628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38264065-38264599 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38264600-38265133 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38266388-38267328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12130 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38270115-38270902 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38270903-38271688 Neighboring gene uncharacterized LOC124904001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8477

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_196057.1 

    Range
    101..260
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    40063008..40063167
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    40926893..40927052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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