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LOC124375236 Sharpr-MPRA regulatory region 1247 [ Homo sapiens (human) ]

Gene ID: 124375236, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124375236
Gene description
Sharpr-MPRA regulatory region 1247
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 DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 8:EnhW). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (131733582..131733876)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (143946499..143946793)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (134608969..134609263)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr9:134426802-134427303 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134443475-134443974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134464737-134465236 Neighboring gene proline rich transmembrane protein 1B Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:134481176-134481676 Neighboring gene Sharpr-MPRA regulatory region 10461 Neighboring gene Rap guanine nucleotide exchange factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134493979-134494945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134499860-134500360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134504170-134504919 Neighboring gene Sharpr-MPRA regulatory region 12258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134530670-134531170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29198 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134534752-134535285 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134535286-134535818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29207 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:134558729-134559329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29208 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:134584807-134585588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134587455-134587956 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134587957-134588456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134598083-134598582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29211 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29212 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29213 Neighboring gene Sharpr-MPRA regulatory region 10210 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29214 Neighboring gene RNA, 7SL, cytoplasmic 328, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134630482-134631089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134669412-134669916 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:134674709-134674899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134680399-134680898 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134682767-134683702 Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134689077-134689577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134692257-134692758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134703449-134703948 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134713047-134713585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134730057-134731006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134731007-134731954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134752115-134752615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:134764767-134765298 Neighboring gene Sharpr-MPRA regulatory region 801 Neighboring gene mediator complex subunit 27 Neighboring gene NANOG hESC enhancer GRCh37_chr9:134840462-134840963 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:134843516-134843723 Neighboring gene MPRA-validated peak7336 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:134882251-134882943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134915689-134916190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:134916191-134916690 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:134917173-134918372 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:134951028-134952227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29216

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_078957.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    131733582..131733876
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    143946499..143946793
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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