Variant report

Variant	rs17075558
Chromosome Location	chr3:43358926-43358927
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43358290..43360924-chr3:43368832..43371042,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10865932	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634274	1.00[CHB][hapmap]
rs13065491	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13320571	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1384433	1.00[CHB][hapmap]
rs1395372	1.00[CHB][hapmap]
rs1588027	1.00[CHB][hapmap]
rs17075317	0.82[JPT][hapmap]
rs17075535	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075596	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075600	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17075630	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17075705	1.00[CHB][hapmap]
rs17075743	1.00[CHB][hapmap]
rs2372372	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2372437	1.00[CHB][hapmap]
rs2888298	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4128529	1.00[CHB][hapmap]
rs4510359	1.00[CHB][hapmap]
rs4586783	1.00[CHB][hapmap]
rs4682678	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4682679	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4682682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4682882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4683366	1.00[JPT][hapmap]
rs6441772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6441777	1.00[CHB][hapmap]
rs6770540	1.00[CHB][hapmap]
rs6783741	1.00[CHB][hapmap]
rs6791641	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6800983	1.00[CHB][hapmap]
rs6803929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621298	0.82[JPT][hapmap]
rs7623883	0.81[ASN][1000 genomes]
rs7628317	1.00[CHB][hapmap]
rs7649401	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311339	1.00[CHB][hapmap]
rs9681394	0.82[JPT][hapmap]
rs977911	1.00[CHB][hapmap]
rs9834842	0.90[CEU][hapmap]
rs9836386	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9876172	0.83[YRI][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	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43330800-43359000	Weak transcription	Fetal Brain Male	brain
2	chr3:43332400-43361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:43332800-43377000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:43340200-43359000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:43340200-43361200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:43340600-43359200	Weak transcription	Gastric	stomach
7	chr3:43340600-43365600	Weak transcription	Esophagus	oesophagus
8	chr3:43341000-43359000	Weak transcription	Spleen	Spleen
9	chr3:43342000-43359200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:43344600-43359400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:43345000-43368200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:43345400-43359000	Weak transcription	Fetal Kidney	kidney
13	chr3:43345400-43367400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:43345600-43360200	Weak transcription	Brain Germinal Matrix	brain
15	chr3:43345600-43364400	Weak transcription	HMEC	breast
16	chr3:43346000-43359000	Weak transcription	NHLF	lung
17	chr3:43346000-43359200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:43346000-43359200	Weak transcription	Ovary	ovary
19	chr3:43346000-43377000	Weak transcription	K562	blood
20	chr3:43346400-43359000	Weak transcription	Fetal Heart	heart
21	chr3:43346400-43367200	Weak transcription	Fetal Lung	lung
22	chr3:43348400-43378800	Weak transcription	Hela-S3	cervix
23	chr3:43349600-43363200	Weak transcription	GM12878-XiMat	blood
24	chr3:43350000-43359000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:43350000-43367400	Weak transcription	Aorta	Aorta
26	chr3:43350400-43359000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:43350400-43361000	Weak transcription	Fetal Brain Female	brain
28	chr3:43350400-43365800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:43350600-43359600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:43351000-43375600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:43351600-43359600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:43352600-43363200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:43353000-43361600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:43353000-43374000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:43353200-43359000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:43353200-43359000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:43353200-43359000	Weak transcription	Right Atrium	heart
38	chr3:43353200-43359200	Weak transcription	Primary B cells from cord blood	blood
39	chr3:43353200-43367400	Weak transcription	Dnd41	blood
40	chr3:43353400-43375200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:43354400-43369600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:43355000-43364600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:43355800-43360400	Genic enhancers	HUVEC	blood vessel
44	chr3:43356000-43360200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:43356000-43362200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:43356000-43362200	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr3:43356200-43359800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:43356200-43362800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr3:43356400-43359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:43356400-43359400	Enhancers	Small Intestine	intestine

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