Variant report

Variant	rs9857489
Chromosome Location	chr3:180324883-180324884
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:180322063..180324042-chr3:180324273..180325867,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1353679	0.91[EUR][1000 genomes]
rs1532485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1603658	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17707963	0.82[EUR][1000 genomes]
rs17708913	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28385473	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28495789	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62291004	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62291005	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62291006	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62291007	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62291008	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62291009	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62291043	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62291045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62291048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6770664	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6774942	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9290705	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9819839	0.84[EUR][1000 genomes]
rs9837678	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9846858	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9847201	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9858483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9864959	0.84[EUR][1000 genomes]
rs9866580	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9872076	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9876153	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9877497	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv1007831	chr3:180162003-180348203	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536818	chr3:180162003-180348203	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3359190	chr3:180298396-180397223	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180320600-180325800	Weak transcription	Lung	lung
2	chr3:180320600-180327000	Weak transcription	Small Intestine	intestine
3	chr3:180320600-180330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:180320600-180337400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:180320600-180343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:180320600-180343800	Weak transcription	Spleen	Spleen
7	chr3:180320600-180344200	Weak transcription	Esophagus	oesophagus
8	chr3:180320600-180344200	Weak transcription	Gastric	stomach
9	chr3:180320800-180327400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:180320800-180344000	Weak transcription	Pancreas	Pancrea
11	chr3:180320800-180344400	Weak transcription	Aorta	Aorta
12	chr3:180321000-180325600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:180321000-180329400	Weak transcription	Stomach Mucosa	stomach
14	chr3:180321000-180330200	Weak transcription	Ovary	ovary
15	chr3:180321000-180334200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:180321200-180326800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:180321200-180327000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:180321200-180327400	Weak transcription	Colonic Mucosa	Colon
19	chr3:180321200-180330600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:180321200-180332000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:180321200-180333000	Strong transcription	HSMM	muscle
22	chr3:180321400-180325800	Weak transcription	Right Ventricle	heart
23	chr3:180321400-180325800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:180321400-180325800	Weak transcription	Thymus	Thymus
25	chr3:180321400-180326000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:180321400-180327400	Weak transcription	Psoas Muscle	Psoas
27	chr3:180321400-180330800	Strong transcription	Placenta	Placenta
28	chr3:180321400-180331800	Strong transcription	Fetal Thymus	thymus
29	chr3:180321400-180331800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr3:180321400-180332400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:180321400-180333800	Weak transcription	Fetal Heart	heart
32	chr3:180321600-180331400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:180321600-180331400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:180321600-180331600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:180321600-180332000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:180321600-180332000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr3:180321600-180332200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:180321600-180332600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:180321600-180333200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:180321600-180333800	Strong transcription	Primary B cells from cord blood	blood
41	chr3:180321600-180342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:180321800-180331000	Strong transcription	Osteobl	bone
43	chr3:180321800-180331400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:180321800-180331400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:180321800-180331400	Strong transcription	Fetal Lung	lung
46	chr3:180321800-180331600	Strong transcription	NHDF-Ad	bronchial
47	chr3:180321800-180331800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:180321800-180331800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:180321800-180331800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:180321800-180332000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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