Variant report

Variant	rs17060881
Chromosome Location	chr3:59521666-59521667
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCTD6-7	chr3:59521589-59522141	NONHSAT090151

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11710236	1.00[ASN][1000 genomes]
rs11716758	1.00[ASN][1000 genomes]
rs1502616	1.00[ASN][1000 genomes]
rs17060864	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17060872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17060880	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17060901	1.00[ASN][1000 genomes]
rs35769758	1.00[ASN][1000 genomes]
rs56188040	1.00[ASN][1000 genomes]
rs57453654	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62250726	1.00[ASN][1000 genomes]
rs62250728	1.00[ASN][1000 genomes]
rs6768376	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798519	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73084821	1.00[ASN][1000 genomes]
rs73837332	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837338	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837342	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837345	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837346	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837349	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837350	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837352	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837356	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857745	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871074	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875227	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011181	chr3:58665373-59542339	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv536574	chr3:58665373-59542339	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv534257	chr3:58855959-59606464	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv876836	chr3:59500394-59664687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59508200-59526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:59517600-59521800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:59517600-59524800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:59518000-59521800	Weak transcription	Pancreas	Pancrea
5	chr3:59518000-59530800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:59518600-59524400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:59520000-59523000	Enhancers	Fetal Heart	heart
8	chr3:59520400-59522400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:59520600-59521800	Enhancers	Colon Smooth Muscle	Colon
10	chr3:59520600-59522400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:59520800-59522800	Enhancers	Osteobl	bone
12	chr3:59520800-59523000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:59521000-59522200	Enhancers	NH-A	brain
14	chr3:59521200-59522400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:59521200-59522800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:59521400-59522000	Enhancers	Rectal Smooth Muscle	rectum
17	chr3:59521400-59522200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:59521400-59522200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:59521400-59522200	Enhancers	HSMMtube	muscle
20	chr3:59521600-59522000	Enhancers	NHLF	lung
21	chr3:59521600-59522200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:59521600-59522200	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:59521600-59522200	Enhancers	HMEC	breast
24	chr3:59521600-59522200	Enhancers	NHEK	skin

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