LOC129995575 (ATAC-STARR-seq lymphoblastoid active region 23845) - Rat Genome Database

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Gene: LOC129995575 (ATAC-STARR-seq lymphoblastoid active region 23845) Homo sapiens
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Symbol: LOC129995575
Name: ATAC-STARR-seq lymphoblastoid active region 23845
RGD ID: 329815067
Description: This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate 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
GRCh386404,970 - 405,089 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376404,970 - 405,089 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.06263,301 - 263,420 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LOC129995575HumanSkin/Hair/Eye Pigmentation, Variation In, 8  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: IRF4-related conditionClinVarPMID:25741868 and PMID:28492532
LOC129995575HumanSkin/Hair/Eye Pigmentation, Variation In, 8  IAGP (Homo sapiens)8554872ClinVar Annotator: match by term: Skin/hair/eye pigmentation more ...ClinVarPMID:25741868

PMID:35858748  



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Variants in LOC129995575
17 total Variants

1 to 10 of 55 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
NM_002460.4(IRF4):c.1162G>A (p.Gly388Arg) single nucleotide variant Skin/hair/eye pigmentation, variation in, 8 [RCV004821362] Chr6:405080 [GRCh38]
Chr6:405080 [GRCh37]
Chr6:6p25.3		 uncertain significance
GRCh38/hg38 6p25.3(chr6:259528-439290)x1 copy number loss See cases [RCV000050817] Chr6:259528..439290 [GRCh38]
Chr6:259528..439290 [GRCh37]
Chr6:204528..384290 [NCBI36]
Chr6:6p25.3		 benign
GRCh38/hg38 6p25.3(chr6:163083-918985)x1 copy number loss See cases [RCV000050372] Chr6:163083..918985 [GRCh38]
Chr6:163083..919234 [GRCh37]
Chr6:108083..864234 [NCBI36]
Chr6:6p25.3		 pathogenic|uncertain significance|conflicting data from submitters
GRCh38/hg38 6p25.3(chr6:163083-1951351)x3 copy number gain See cases [RCV000050603] Chr6:163083..1951351 [GRCh38]
Chr6:163083..1951585 [GRCh37]
Chr6:108083..1896584 [NCBI36]
Chr6:6p25.3		 pathogenic
GRCh38/hg38 6p25.3-24.1(chr6:164360-13339881)x3 copy number gain See cases [RCV000134022] Chr6:164360..13339881 [GRCh38]
Chr6:164360..13340113 [GRCh37]
Chr6:109360..13448092 [NCBI36]
Chr6:6p25.3-24.1		 pathogenic
NM_002460.4(IRF4):c.1119C>G (p.His373Gln) single nucleotide variant not provided [RCV001948898] Chr6:405037 [GRCh38]
Chr6:405037 [GRCh37]
Chr6:6p25.3		 uncertain significance
NM_002460.4(IRF4):c.1127G>A (p.Arg376His) single nucleotide variant IRF4-related disorder [RCV003418283]|not provided [RCV002038087] Chr6:405045 [GRCh38]
Chr6:405045 [GRCh37]
Chr6:6p25.3		 uncertain significance
GRCh38/hg38 6p25.3-25.1(chr6:163083-6062800)x1 copy number loss See cases [RCV000050686] Chr6:163083..6062800 [GRCh38]
Chr6:163083..6063033 [GRCh37]
Chr6:108083..6008032 [NCBI36]
Chr6:6p25.3-25.1		 pathogenic
NM_002460.4(IRF4):c.1154T>A (p.Leu385Gln) single nucleotide variant not provided [RCV002050115] Chr6:405072 [GRCh38]
Chr6:405072 [GRCh37]
Chr6:6p25.3		 uncertain significance
NM_002460.4(IRF4):c.1126C>T (p.Arg376Cys) single nucleotide variant not provided [RCV001997000] Chr6:405044 [GRCh38]
Chr6:405044 [GRCh37]
Chr6:6p25.3		 uncertain significance
1 to 10 of 55 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
2289408BW324_HBody weight QTL 324 (human)3.150.0001Body fat amount6120803913Human
1643418BW282_HBody Weight QTL 282 (human)2.070.001Body weight6119321359Human
2289435BMD4_HBone mineral density QTL 4 (human)3.150.0001Bone mineral density6120803913Human
2292824PRSTS5_HProstate tumor susceptibility QTL 5 (human)Prostate tumor susceptibility6119232373Human
2289320BW390_HBody weight QTL 390 (human)2.13Body weightBMI6119321359Human
1643495BW291_HBody Weight QTL 291 (human)2.13Body weightBMI6119321359Human
RefSeq Transcripts NG_175021 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL589962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles



Database
Acc Id
Source(s)
COSMIC LOC129995575 COSMIC
GTEx LOC129995575 GTEx
Human Proteome Map LOC129995575 Human Proteome Map
NCBI Gene LOC129995575 ENTREZGENE