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LOC130061614 ATAC-STARR-seq lymphoblastoid silent region 8936 [ Homo sapiens (human) ]

Gene ID: 130061614, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061614
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8936
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 LOC130061614 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 (74736742..74736911)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (75628620..75628789)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (72732881..72733050)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371894 Neighboring gene RAB37, member RAS oncogene family Neighboring gene CD300 molecule like family member f Neighboring gene uncharacterized LOC124904057 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12715 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72733027-72733750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:72734475-72735197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12717 Neighboring gene SLC9A3R1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:72743321-72743916 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72745205-72745830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:72747322-72747863 Neighboring gene microRNA 3615 Neighboring gene NHERF family PDZ scaffold protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72753485-72754231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72754232-72754979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72754980-72755726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72755727-72756474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:72759127-72759878 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12718 Neighboring gene N-acetyltransferase 9

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_196758.1 

    Range
    101..270
    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
    74736742..74736911
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    75628620..75628789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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