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LOC130062024 ATAC-STARR-seq lymphoblastoid silent region 9206 [ Homo sapiens (human) ]

Gene ID: 130062024, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130062024
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9206
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 LOC130062024 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 (82273630..82273839)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83142367..83142576)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80231506..80231715)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 57 Neighboring gene uncharacterized LOC124904119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12990 Neighboring gene Sharpr-MPRA regulatory region 9641 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80131430-80132220 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80133010-80133799 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80137557-80138524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80138525-80139491 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:80163065-80163866 and GRCh37_chr17:80163867-80164668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80171129-80172071 Neighboring gene Sharpr-MPRA regulatory region 4733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12994 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:80183365-80183517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9197 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9202 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9203 Neighboring gene solute carrier family 16 member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12995 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80195135-80195906 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80196677-80197447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12996 Neighboring gene microRNA 6787 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:80210177-80211376 Neighboring gene casein kinase 1 delta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80223561-80224292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9204 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9205 Neighboring gene uncharacterized LOC124904089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80234577-80235076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12997 Neighboring gene CSNK1D-CD7 intergenic CAGE-defined low expression enhancer Neighboring gene long intergenic non-protein coding RNA 1970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80261261-80261761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80272095-80272682 Neighboring gene CD7 molecule

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_197105.1 

    Range
    101..310
    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
    82273630..82273839
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    83142367..83142576
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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