Variant report

Variant	rs2199503
Chromosome Location	chr3:119778489-119778490
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	chr3:119774518..119780956-chr3:119811182..119816004,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10433404	0.82[JPT][hapmap]
rs10934502	0.82[JPT][hapmap]
rs10934503	0.81[JPT][hapmap]
rs10934505	0.82[JPT][hapmap]
rs10934506	0.82[JPT][hapmap]
rs1154595	0.91[JPT][hapmap]
rs11921360	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12629015	0.82[JPT][hapmap]
rs12630592	0.91[JPT][hapmap]
rs12634476	0.82[JPT][hapmap]
rs12634889	0.81[JPT][hapmap]
rs12638973	0.81[JPT][hapmap]
rs13321783	0.91[JPT][hapmap]
rs1574154	0.82[JPT][hapmap]
rs1719894	0.91[JPT][hapmap]
rs17204878	0.91[JPT][hapmap]
rs1732170	0.90[JPT][hapmap]
rs1870931	0.82[JPT][hapmap]
rs2319398	0.91[JPT][hapmap]
rs2319399	0.91[JPT][hapmap]
rs28536662	0.91[JPT][hapmap]
rs334533	0.91[JPT][hapmap]
rs334563	0.91[JPT][hapmap]
rs4340737	0.82[JPT][hapmap]
rs4687890	0.91[JPT][hapmap]
rs4687893	0.91[JPT][hapmap]
rs4688042	0.82[JPT][hapmap]
rs4688046	0.82[JPT][hapmap]
rs4688047	0.82[JPT][hapmap]
rs4688054	0.82[JPT][hapmap]
rs6438552	0.91[JPT][hapmap]
rs6438553	0.91[JPT][hapmap]
rs6774210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs6781942	0.91[JPT][hapmap]
rs6782799	0.90[JPT][hapmap]
rs6792572	0.91[JPT][hapmap]
rs6795653	0.91[JPT][hapmap]
rs6800622	0.91[JPT][hapmap]
rs7431209	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs7633279	0.82[JPT][hapmap]
rs7639388	0.82[JPT][hapmap]
rs7644234	0.91[JPT][hapmap]
rs9813864	0.90[JPT][hapmap]
rs9873477	0.91[JPT][hapmap]
rs9878473	0.91[JPT][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119759400-119786200	Weak transcription	Hela-S3	cervix
2	chr3:119760200-119779400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:119760200-119805400	Weak transcription	HMEC	breast
4	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:119768800-119792800	Weak transcription	Fetal Stomach	stomach
6	chr3:119769200-119780600	Weak transcription	Aorta	Aorta
7	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:119769800-119784800	Weak transcription	Dnd41	blood
9	chr3:119771400-119779200	Weak transcription	Right Atrium	heart
10	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:119771600-119778800	Weak transcription	Fetal Heart	heart
12	chr3:119771800-119778800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:119771800-119781800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:119771800-119783600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:119771800-119805400	Weak transcription	NHEK	skin
16	chr3:119772000-119779200	Weak transcription	Ovary	ovary
17	chr3:119772400-119778800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
19	chr3:119773800-119787800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:119774000-119789600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:119775400-119782600	Weak transcription	Esophagus	oesophagus
22	chr3:119775800-119779200	Weak transcription	Left Ventricle	heart
23	chr3:119775800-119784200	Weak transcription	Fetal Intestine Small	intestine
24	chr3:119775800-119790400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:119775800-119796000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:119775800-119797600	Weak transcription	Fetal Thymus	thymus
27	chr3:119776000-119779000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:119776400-119779400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:119776600-119779200	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:119777200-119779600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:119777200-119780000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:119777400-119779200	Weak transcription	Small Intestine	intestine
33	chr3:119777400-119779400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:119777400-119780000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:119777600-119778800	Enhancers	Primary B cells from cord blood	blood
36	chr3:119777800-119778800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:119777800-119779000	Enhancers	Brain Angular Gyrus	brain
38	chr3:119777800-119779600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:119777800-119779600	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:119777800-119779800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:119777800-119779800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:119778000-119778600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:119778000-119779000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:119778000-119779000	Flanking Active TSS	GM12878-XiMat	blood
45	chr3:119778000-119779200	Enhancers	Adipose Nuclei	Adipose
46	chr3:119778000-119779200	Weak transcription	Lung	lung
47	chr3:119778000-119779400	Enhancers	Brain Anterior Caudate	brain
48	chr3:119778000-119779400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr3:119778000-119779400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:119778000-119779600	Enhancers	Cortex derived primary cultured neurospheres	brain

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