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LOC130056689 ATAC-STARR-seq lymphoblastoid silent region 6240 [ Homo sapiens (human) ]

Gene ID: 130056689, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056689
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6240
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 LOC130056689 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (105473884..105473973)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (99721011..99721100)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (105940221..105940310)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105884361-105885030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105887709-105888376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105888377-105889046 Neighboring gene MTA1 divergent transcript Neighboring gene metastasis associated 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105903142-105903739 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:105903740-105904336 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105930591-105931113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105931114-105931635 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105937181-105938044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105939600-105940132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6242 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6243 Neighboring gene cysteine rich protein 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105947154-105947875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:105954409-105954980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6250 Neighboring gene hESC enhancers GRCh37_chr14:105956919-105957662 and GRCh37_chr14:105957663-105958406 Neighboring gene cysteine rich protein 1 Neighboring gene Sharpr-MPRA regulatory region 9919 Neighboring gene tubulin epsilon and delta complex 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_191110.1 

    Range
    101..190
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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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    105473884..105473973
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    99721011..99721100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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