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LOC130061894 ATAC-STARR-seq lymphoblastoid silent region 9097 [ Homo sapiens (human) ]

Gene ID: 130061894, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061894
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9097
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 LOC130061894 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 (79991673..79991732)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (80889612..80889671)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (77965472..77965531)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1979 Neighboring gene long intergenic non-protein coding RNA 1978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917109-77917834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77917835-77918560 Neighboring gene TBC1 domain family member 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77921171-77921997 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922367-77922950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77922951-77923534 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77923535-77924118 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77924703-77925286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:77925287-77925870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77930057-77930557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77948310-77949214 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77951994-77952173 Neighboring gene uncharacterized LOC124904073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77961646-77962517 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77966696-77967895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77975818-77976678 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77987013-77987179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77996703-77997568 Neighboring gene uncharacterized LOC124904072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78003463-78004332 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12927 Neighboring gene Sharpr-MPRA regulatory region 13982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78018463-78018964 Neighboring gene coiled-coil domain 40 molecular ruler complex subunit Neighboring gene uncharacterized LOC124904074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78039691-78040515

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_196995.1 

    Range
    101..160
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    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
    79991673..79991732
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791802.1 Reference GRCh38.p14 PATCHES

    Range
    14584..14643
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    80889612..80889671
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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