LOC130057031 (ATAC-STARR-seq lymphoblastoid silent region 6422) - Rat Genome Database

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Gene: LOC130057031 (ATAC-STARR-seq lymphoblastoid silent region 6422) Homo sapiens
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Symbol: LOC130057031
Name: ATAC-STARR-seq lymphoblastoid silent region 6422
RGD ID: 329817867
Description: 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]
Type: biological-region
RefSeq Status: REVIEWED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381549,190,761 - 49,190,820 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371549,482,958 - 49,483,017 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.01546,998,954 - 46,999,013 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


PMID:35858748  



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1 to 10 of 82 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 19p13.11-q13.11(chr19:17176767-34924150)x3 copy number gain See cases [RCV000050635] Chr19:17176767..34924150 [GRCh38]
Chr19:17287576..35415054 [GRCh37]
Chr19:17148576..40106894 [NCBI36]
Chr19:19p13.11-q13.11		 pathogenic
GRCh38/hg38 19p13.12-q11(chr19:13974677-27839676)x3 copy number gain See cases [RCV000052912] Chr19:13974677..27839676 [GRCh38]
Chr19:14085489..28330584 [GRCh37]
Chr19:13946489..33022424 [NCBI36]
Chr19:19p13.12-q11		 pathogenic
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31		 pathogenic
GRCh38/hg38 19p13.12-12(chr19:15133594-24193591)x3 copy number gain See cases [RCV000136696] Chr19:15133594..24193591 [GRCh38]
Chr19:15244405..24376393 [GRCh37]
Chr19:15105405..24168233 [NCBI36]
Chr19:19p13.12-12		 pathogenic|likely pathogenic
GRCh38/hg38 19p12(chr19:20637987-21976216)x3 copy number gain See cases [RCV000142012] Chr19:20637987..21976216 [GRCh38]
Chr19:20820793..22159018 [GRCh37]
Chr19:20612633..21950858 [NCBI36]
Chr19:19p12		 uncertain significance
chr19:19230868-24115369 complex variant complex Breast ductal adenocarcinoma [RCV000207223] Chr19:19230868..24115369 [GRCh37]
Chr19:19p13.11-12		 uncertain significance
NM_001076678.3(ZNF493):c.667T>A (p.Ser223Thr) single nucleotide variant not specified [RCV004285687] Chr19:21423326 [GRCh38]
Chr19:21606128 [GRCh37]
Chr19:19p12		 uncertain significance
GRCh37/hg19 19p13.11-11(chr19:16526787-24631604)x3 copy number gain not provided [RCV000752593] Chr19:16526787..24631604 [GRCh37]
Chr19:19p13.11-11		 pathogenic
GRCh37/hg19 19p12(chr19:21567360-21686650)x1 copy number loss not provided [RCV000752624] Chr19:21567360..21686650 [GRCh37]
Chr19:19p12		 benign
GRCh37/hg19 19p12(chr19:21581064-21609065)x3 copy number gain See cases [RCV000446100] Chr19:21581064..21609065 [GRCh37]
Chr19:19p12		 likely benign
1 to 10 of 82 rows

The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1643273BW330_HBody Weight QTL 330 (human)1.050.014Body weightbody mass index152686671952866719Human
1559411SCL107_HSerum cholesterol level QTL 107 (human)3.88Lipid leveltriglyceride152654355252543552Human
2299958PRSTS330_HProstate tumor susceptibility QTL 330 (human)1.020.0151Prostate tumor susceptibility153479023060790230Human
1559354LDLPS4_HLow density lipoprotein particle size QTL 4 (human)2.20.019LDL particle size153479023060790230Human
RefSeq Transcripts NG_191452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC013452 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles



Database
Acc Id
Source(s)
COSMIC LOC130057031 COSMIC
GTEx LOC130057031 GTEx
Human Proteome Map LOC130057031 Human Proteome Map
NCBI Gene LOC130057031 ENTREZGENE