Variant report

Variant	rs4129669
Chromosome Location	chr1:56289523-56289524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCSK9-4	chr1:56289480-56289574	XLOC_000207
2	lnc-PCSK9-4	chr1:56289440-56289574	XLOC_000207
3	lnc-PCSK9-4	chr1:56289505-56289574	XLOC_000207
4	lnc-PCSK9-4	chr1:56289431-56289574	NONHSAT003421
5	lnc-PCSK9-4	chr1:56289421-56289574	NONHSAT003420

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10158230	0.81[EUR][1000 genomes]
rs11206668	0.81[EUR][1000 genomes]
rs11206669	0.81[EUR][1000 genomes]
rs11206670	0.82[EUR][1000 genomes]
rs11206671	0.81[EUR][1000 genomes]
rs12132347	0.84[AFR][1000 genomes]
rs12727910	0.83[EUR][1000 genomes]
rs12728204	0.84[EUR][1000 genomes]
rs12729235	0.82[ASN][1000 genomes]
rs3924189	0.82[EUR][1000 genomes]
rs3935996	0.87[EUR][1000 genomes]
rs4309021	0.81[EUR][1000 genomes]
rs4540693	0.81[EUR][1000 genomes]
rs4589149	0.81[EUR][1000 genomes]
rs4926698	0.81[EUR][1000 genomes]
rs6663328	0.81[EUR][1000 genomes]
rs7539074	0.81[EUR][1000 genomes]
rs7546553	0.81[EUR][1000 genomes]
rs7549389	0.87[EUR][1000 genomes]
rs9633424	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829926	chr1:56188492-56360745	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a
2	nsv1002958	chr1:56278696-56295112	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4129669	HSPB11	cis	parietal	SCAN
rs4129669	TMEM59	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56280400-56291000	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:56283000-56293000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:56283200-56292400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:56286800-56290200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:56287800-56290600	Weak transcription	Fetal Kidney	kidney
6	chr1:56287800-56291000	Enhancers	Fetal Intestine Large	intestine
7	chr1:56288000-56290200	Enhancers	Fetal Intestine Small	intestine
8	chr1:56288000-56292000	Enhancers	Fetal Lung	lung
9	chr1:56288400-56290400	Enhancers	NHDF-Ad	bronchial
10	chr1:56288600-56289600	Enhancers	Fetal Stomach	stomach
11	chr1:56288600-56289800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:56288600-56289800	Enhancers	NHLF	lung
13	chr1:56289000-56289600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:56289000-56289600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:56289000-56289600	Enhancers	Osteobl	bone
16	chr1:56289000-56289800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:56289000-56289800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:56289000-56289800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:56289000-56289800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:56289000-56289800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:56289000-56289800	Enhancers	Placenta	Placenta
22	chr1:56289000-56289800	Enhancers	HSMMtube	muscle
23	chr1:56289000-56289800	Enhancers	NH-A	brain
24	chr1:56289200-56289800	Enhancers	A549	lung
25	chr1:56289400-56289600	Enhancers	Pancreas	Pancrea
26	chr1:56289400-56289800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:56289400-56290200	Enhancers	HepG2	liver
28	chr1:56289400-56292800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links