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LOC130061138 ATAC-STARR-seq lymphoblastoid silent region 8677 [ Homo sapiens (human) ]

Gene ID: 130061138, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061138
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8677
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 LOC130061138 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 (49993806..49993855)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (50856946..50856995)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (48071170..48071219)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12375 Neighboring gene RNA, U6 small nuclear 1313, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48048476-48049098 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48049099-48049721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48053397-48053960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48053961-48054524 Neighboring gene distal-less homeobox 4 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr17:48061323-48061824 and GRCh37_chr17:48061825-48062324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48066497-48066998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48066999-48067498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48072293-48072875 Neighboring gene distal-less homeobox 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48111925-48112721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48125618-48126247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48131902-48132428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8678 Neighboring gene p53 inducible cancer associated RNA transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48139516-48140016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48140017-48140517 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:48141472-48142671 Neighboring gene integrin subunit alpha 3

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_196350.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    49993806..49993855
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    50856946..50856995
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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