Variant report

Variant	rs59906228
Chromosome Location	chr3:98583981-98583982
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084679	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13317610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318960	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13320266	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320890	0.97[EUR][1000 genomes]
rs13322253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28417568	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28429424	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28489284	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes]
rs28821579	0.82[EUR][1000 genomes]
rs3796133	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56172805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857413	0.94[ASN][1000 genomes]
rs57962467	0.94[ASN][1000 genomes]
rs72932691	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72932700	0.83[ASN][1000 genomes]
rs72934623	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72934641	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72938577	0.94[ASN][1000 genomes]
rs9289699	0.85[AMR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes]
rs9810407	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812438	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818215	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819309	0.82[EUR][1000 genomes]
rs9828045	0.82[EUR][1000 genomes]
rs9833945	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836915	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838166	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838238	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838706	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9839559	0.91[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9848583	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862660	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9870500	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870940	0.85[AMR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9883751	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv3323873	chr3:98581162-98585460	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
7	esv3440308	chr3:98582662-98587060	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98536200-98594200	Weak transcription	HepG2	liver
2	chr3:98537000-98592800	Weak transcription	K562	blood
3	chr3:98553000-98590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:98575200-98590200	Weak transcription	HSMMtube	muscle
6	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:98575800-98593200	Weak transcription	HUVEC	blood vessel
8	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:98576000-98589800	Weak transcription	HMEC	breast
11	chr3:98576000-98590400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:98576000-98598600	Weak transcription	Fetal Kidney	kidney
13	chr3:98577200-98598800	Weak transcription	Left Ventricle	heart
14	chr3:98578000-98587400	Weak transcription	NHEK	skin
15	chr3:98578000-98588800	Weak transcription	NHLF	lung
16	chr3:98578000-98590400	Weak transcription	Adipose Nuclei	Adipose
17	chr3:98578000-98601000	Weak transcription	Lung	lung
18	chr3:98578200-98586400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:98578200-98590400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:98578400-98586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:98578800-98584000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:98578800-98589200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:98579200-98584000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:98581800-98584000	Weak transcription	NHDF-Ad	bronchial
25	chr3:98582800-98584400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:98583000-98584400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:98583000-98584400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:98583000-98584600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:98583200-98584400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:98583600-98584200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:98583600-98584400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:98583600-98584400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:98583600-98584400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:98583600-98584400	ZNF genes & repeats	Dnd41	blood
36	chr3:98583600-98584400	Strong transcription	Osteobl	bone
37	chr3:98583600-98584600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:98583600-98584600	ZNF genes & repeats	A549	lung
39	chr3:98583600-98584600	Strong transcription	NH-A	brain
40	chr3:98583600-98584800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:98583800-98584400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
42	chr3:98583800-98584400	Strong transcription	HSMM	muscle
43	chr3:98583800-98584600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:98583800-98584800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
45	chr3:98583800-98590800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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