LOC129997708 (ATAC-STARR-seq lymphoblastoid active region 25464) - Rat Genome Database

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Gene: LOC129997708 (ATAC-STARR-seq lymphoblastoid active region 25464) Homo sapiens
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Symbol: LOC129997708
Name: ATAC-STARR-seq lymphoblastoid active region 25464
RGD ID: 329826471
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
GRCh386169,701,583 - 169,701,662 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376170,101,679 - 170,101,758 (+)NCBIGRCh37GRCh37hg19GRCh37
T2T-CHM13v2.06171,055,497 - 171,055,576 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:35858748  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6q27(chr6:164790270-170612001)x1 copy number loss See cases [RCV000135415] Chr6:164790270..170612001 [GRCh38]
Chr6:165203779..170921089 [GRCh37]
Chr6:165123769..170763014 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q25.3-27(chr6:160484810-170612011)x1 copy number loss See cases [RCV000134021] Chr6:160484810..170612011 [GRCh38]
Chr6:160905842..170921099 [GRCh37]
Chr6:160825832..170763024 [NCBI36]
Chr6:6q25.3-27		 pathogenic
GRCh38/hg38 6q27(chr6:168524169-170612001)x1 copy number loss See cases [RCV000050982] Chr6:168524169..170612001 [GRCh38]
Chr6:168924849..170921089 [GRCh37]
Chr6:168667698..170763014 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q27(chr6:169441378-170612001)x1 copy number loss See cases [RCV000050605] Chr6:169441378..170612001 [GRCh38]
Chr6:169841473..170921089 [GRCh37]
Chr6:169583398..170763014 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q27(chr6:169641704-170612001)x1 copy number loss See cases [RCV000051219] Chr6:169641704..170612001 [GRCh38]
Chr6:170041800..170921089 [GRCh37]
Chr6:169783725..170763014 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q27(chr6:169688809-170583214)x1 copy number loss See cases [RCV000136831] Chr6:169688809..170583214 [GRCh38]
Chr6:170088905..170892302 [GRCh37]
Chr6:169830830..170734227 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q25.2-27(chr6:154539655-170714507)x1 copy number loss See cases [RCV000137381] Chr6:154539655..170714507 [GRCh38]
Chr6:154860789..171023595 [GRCh37]
Chr6:154902481..170865520 [NCBI36]
Chr6:6q25.2-27		 pathogenic
GRCh38/hg38 6q26-27(chr6:161349282-170584790)x1 copy number loss Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures [RCV003327715] Chr6:161349282..170584790 [GRCh38]
Chr6:6q26-27		 pathogenic
GRCh38/hg38 6q27(chr6:167963618-170597678)x1 copy number loss See cases [RCV000139526] Chr6:167963618..170597678 [GRCh38]
Chr6:168364298..170906766 [GRCh37]
Chr6:168107147..170748691 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q27(chr6:168581259-170610394)x1 copy number loss See cases [RCV000140451] Chr6:168581259..170610394 [GRCh38]
Chr6:168981939..170919482 [GRCh37]
Chr6:168724788..170761407 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q27(chr6:167145050-170714507)x1 copy number loss See cases [RCV000137523] Chr6:167145050..170714507 [GRCh38]
Chr6:167558538..171023595 [GRCh37]
Chr6:167478528..170865520 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q25.3-27(chr6:159915390-170714507)x1 copy number loss See cases [RCV000139636] Chr6:159915390..170714507 [GRCh38]
Chr6:160336422..171023595 [GRCh37]
Chr6:160256412..170865520 [NCBI36]
Chr6:6q25.3-27		 pathogenic
GRCh38/hg38 6q27(chr6:168802993-170714507)x1 copy number loss See cases [RCV000137643] Chr6:168802993..170714507 [GRCh38]
Chr6:169203088..171023595 [GRCh37]
Chr6:168945013..170865520 [NCBI36]
Chr6:6q27		 likely pathogenic
GRCh38/hg38 6q26-27(chr6:160899898-170610394)x1 copy number loss See cases [RCV000143619] Chr6:160899898..170610394 [GRCh38]
Chr6:161320930..170919482 [GRCh37]
Chr6:161240920..170761407 [NCBI36]
Chr6:6q26-27		 pathogenic
GRCh38/hg38 6q25.2-27(chr6:154118058-170602152)x1 copy number loss See cases [RCV000052207] Chr6:154118058..170602152 [GRCh38]
Chr6:154439193..170911240 [GRCh37]
Chr6:154480885..170753165 [NCBI36]
Chr6:6q25.2-27		 pathogenic
GRCh38/hg38 6q26-27(chr6:162042846-170608818)x1 copy number loss See cases [RCV000052223] Chr6:162042846..170608818 [GRCh38]
Chr6:162463878..170917906 [GRCh37]
Chr6:162383868..170759831 [NCBI36]
Chr6:6q26-27		 pathogenic
GRCh38/hg38 6q26-27(chr6:163420224-170608818)x1 copy number loss See cases [RCV000052225] Chr6:163420224..170608818 [GRCh38]
Chr6:163841256..170917906 [GRCh37]
Chr6:163761246..170759831 [NCBI36]
Chr6:6q26-27		 pathogenic
GRCh38/hg38 6q27(chr6:168180473-170583214)x1 copy number loss See cases [RCV000052230] Chr6:168180473..170583214 [GRCh38]
Chr6:168581153..170892302 [GRCh37]
Chr6:168324002..170734227 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q25.3-27(chr6:159454639-170612001)x1 copy number loss See cases [RCV000052209] Chr6:159454639..170612001 [GRCh38]
Chr6:159875671..170921089 [GRCh37]
Chr6:159795661..170763014 [NCBI36]
Chr6:6q25.3-27		 pathogenic
GRCh38/hg38 6q27(chr6:167924952-170602152)x1 copy number loss See cases [RCV000052229] Chr6:167924952..170602152 [GRCh38]
Chr6:168325632..170911240 [GRCh37]
Chr6:168068481..170753165 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q27(chr6:168881467-170602152)x1 copy number loss See cases [RCV000137746] Chr6:168881467..170602152 [GRCh38]
Chr6:169281562..170911240 [GRCh37]
Chr6:169023487..170753165 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q27(chr6:167760366-170610394)x1 copy number loss See cases [RCV000143582] Chr6:167760366..170610394 [GRCh38]
Chr6:168161046..170919482 [GRCh37]
Chr6:167903895..170761407 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q25.3-27(chr6:159825913-170612001)x1 copy number loss See cases [RCV000052211] Chr6:159825913..170612001 [GRCh38]
Chr6:160246945..170921089 [GRCh37]
Chr6:160166935..170763014 [NCBI36]
Chr6:6q25.3-27		 pathogenic
GRCh38/hg38 6q25.3-27(chr6:160359686-170608818)x1 copy number loss See cases [RCV000052213] Chr6:160359686..170608818 [GRCh38]
Chr6:160780718..170917906 [GRCh37]
Chr6:160700708..170759831 [NCBI36]
Chr6:6q25.3-27		 pathogenic
GRCh38/hg38 6q26-27(chr6:162789915-170602152)x1 copy number loss See cases [RCV000052224] Chr6:162789915..170602152 [GRCh38]
Chr6:163210947..170911240 [GRCh37]
Chr6:163130937..170753165 [NCBI36]
Chr6:6q26-27		 pathogenic
GRCh38/hg38 6q27(chr6:169021176-170602152)x1 copy number loss See cases [RCV000052243] Chr6:169021176..170602152 [GRCh38]
Chr6:169421271..170911240 [GRCh37]
Chr6:169163196..170753165 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q25.2-27(chr6:152793402-170610394)x1 copy number loss See cases [RCV000141880] Chr6:152793402..170610394 [GRCh38]
Chr6:153114537..170919482 [GRCh37]
Chr6:153156230..170761407 [NCBI36]
Chr6:6q25.2-27		 pathogenic
GRCh38/hg38 6q27(chr6:167896913-170714507)x1 copy number loss See cases [RCV000140812] Chr6:167896913..170714507 [GRCh38]
Chr6:168297593..171023595 [GRCh37]
Chr6:168040442..170865520 [NCBI36]
Chr6:6q27		 pathogenic
GRCh38/hg38 6q25.2-27(chr6:152376338-170612001)x3 copy number gain See cases [RCV000142594] Chr6:152376338..170612001 [GRCh38]
Chr6:152697473..170921089 [GRCh37]
Chr6:152739166..170763014 [NCBI36]
Chr6:6q25.2-27		 pathogenic
GRCh38/hg38 6q27(chr6:166370159-170602152)x1 copy number loss See cases [RCV000052227] Chr6:166370159..170602152 [GRCh38]
Chr6:166783647..170911240 [GRCh37]
Chr6:166703637..170753165 [NCBI36]
Chr6:6q27		 pathogenic

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1643404BMD3_HBone mineral density QTL 3 (human)2.420.0005Bone mineral density6157563614170805979Human
1643367BW323_HBody weight QTL 323 (human)2.420.0005Body fat amount6157563614170805979Human


Expression

RNA-SEQ Expression


Sequence



Additional Information

Database Acc Id Source(s)
COSMIC LOC129997708 COSMIC
GTEx LOC129997708 GTEx
Human Proteome Map LOC129997708 Human Proteome Map
NCBI Gene LOC129997708 ENTREZGENE