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LOC123575678 Sharpr-MPRA regulatory region 9195 [ Homo sapiens (human) ]

Gene ID: 123575678, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575678
Gene description
Sharpr-MPRA regulatory region 9195
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 was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123575678 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (14819038..14819332)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (14692194..14692488)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (14819269..14819563)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928354 Neighboring gene uncharacterized LOC102724463 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24053 Neighboring gene RNA, U6 small nuclear 793, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14676877-14677412 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14706129-14707328 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24054 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:14730658-14731857 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14733080-14734279 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16945 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:14743342-14744541 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14784175-14784726 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr6:14784727-14785278 and GRCh37_chr6:14785279-14785830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14804615-14805450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24056 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14822305-14822806 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14823177-14823964 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14824752-14825538 Neighboring gene NANOG hESC enhancer GRCh37_chr6:14832080-14832596 Neighboring gene Sharpr-MPRA regulatory region 9180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24057 Neighboring gene uncharacterized LOC105374945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14876936-14877436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14879976-14880486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:14880487-14880996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:14883452-14884163 Neighboring gene MPRA-validated peak5674 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24062 Neighboring gene MPRA-validated peak5675 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:14958411-14958600 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:14997283-14997782 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15013597-15013834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15017607-15018302 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15021466-15022336 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15022337-15023206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24063 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:15066479-15067678 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15077925-15078456 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15096502-15096739 Neighboring gene ribosomal protein L6 pseudogene 17

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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_077937.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    14819038..14819332
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    14692194..14692488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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