Variant report

Variant	rs12117312
Chromosome Location	chr1:56101264-56101265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56100834..56102413-chr1:56105064..56106750,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCSK9-8	chr1:56101193-56101320	NONHSAT003418

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10443236	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10749702	0.82[CEU][hapmap]
rs11206636	0.82[CEU][hapmap]
rs11206647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11206648	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11206650	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12026971	0.82[CEU][hapmap]
rs12039713	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12124393	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12132336	0.82[CEU][hapmap]
rs12405865	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1392130	0.82[CEU][hapmap]
rs1392132	0.82[CEU][hapmap]
rs1499670	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17418669	0.87[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1955318	0.85[CEU][hapmap]
rs2671238	0.81[CEU][hapmap]
rs7555929	0.84[CEU][hapmap]
rs9326036	0.82[CEU][hapmap]
rs9436522	0.84[CEU][hapmap]
rs9436526	0.82[CEU][hapmap]
rs9436984	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56089000-56104000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:56096000-56103400	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:56096800-56102800	Enhancers	Osteobl	bone
4	chr1:56097000-56103000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:56097000-56103400	Enhancers	NHDF-Ad	bronchial
6	chr1:56098000-56101800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:56098400-56102200	Enhancers	NHLF	lung
8	chr1:56098800-56105800	Weak transcription	Fetal Stomach	stomach
9	chr1:56099000-56105200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:56099000-56106600	Weak transcription	Ovary	ovary
11	chr1:56099200-56105800	Weak transcription	Fetal Kidney	kidney
12	chr1:56099400-56101600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:56099600-56101800	Enhancers	Aorta	Aorta
14	chr1:56100000-56102600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:56100600-56101600	Weak transcription	Fetal Lung	lung
16	chr1:56100600-56102400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:56100600-56106600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:56100800-56102400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:56100800-56104800	Weak transcription	Hela-S3	cervix
20	chr1:56100800-56106600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:56101200-56104200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:56101200-56105000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:56101200-56105800	Weak transcription	Psoas Muscle	Psoas

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