Variant report

Variant	rs17005712
Chromosome Location	chr3:69416837-69416838
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	chr3:69416233..69418620-chr3:69433830..69435946,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114541	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13320477	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17005675	0.92[CEU][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005685	1.00[CEU][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005687	1.00[CEU][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17005689	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005691	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17005694	1.00[CEU][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17005696	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17005699	1.00[CEU][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17005713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17416638	0.81[AMR][1000 genomes]
rs2314987	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs2872808	0.85[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4241387	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4855394	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5026329	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56653941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56682655	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57343519	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58937767	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59683429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60969945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72940765	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72940769	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72940771	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72940775	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72940779	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72940783	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72940785	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs881031	0.85[CEU][hapmap];0.86[MKK][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs964553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[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	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv520818	chr3:69401248-69421495	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2760780	chr3:69413876-69513947	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1946491	chr3:69416537-69416929	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69402200-69419000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:69410200-69417400	Weak transcription	Fetal Lung	lung
3	chr3:69413600-69417200	Weak transcription	Aorta	Aorta
4	chr3:69413600-69417200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:69413600-69417200	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:69413600-69417200	Weak transcription	Fetal Thymus	thymus
7	chr3:69413600-69417400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:69413600-69417400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:69413600-69417400	Weak transcription	Brain Substantia Nigra	brain
10	chr3:69413600-69417600	Weak transcription	Esophagus	oesophagus
11	chr3:69413600-69418000	Weak transcription	HSMMtube	muscle
12	chr3:69413600-69419000	Weak transcription	NHDF-Ad	bronchial
13	chr3:69413800-69417000	Weak transcription	HUVEC	blood vessel
14	chr3:69413800-69417400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:69413800-69417600	Weak transcription	Placenta	Placenta
16	chr3:69413800-69417600	Weak transcription	Right Atrium	heart
17	chr3:69413800-69419000	Weak transcription	Brain Angular Gyrus	brain
18	chr3:69413800-69419400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:69414000-69417200	Weak transcription	Thymus	Thymus
20	chr3:69414000-69417400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:69414000-69417400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:69414000-69418400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:69414000-69419000	Weak transcription	Osteobl	bone
24	chr3:69414200-69418000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:69414600-69417000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:69414600-69417400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:69414800-69417200	Weak transcription	HMEC	breast
28	chr3:69414800-69417200	Weak transcription	NHEK	skin
29	chr3:69415000-69417200	Weak transcription	HSMM	muscle
30	chr3:69415000-69417400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:69415000-69417400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:69415000-69418800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:69415200-69417200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:69415400-69417200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:69415400-69417400	Weak transcription	Lung	lung
36	chr3:69415800-69417200	Enhancers	Dnd41	blood
37	chr3:69416000-69419000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:69416000-69419200	Weak transcription	Fetal Brain Male	brain
39	chr3:69416400-69417000	Enhancers	Primary hematopoietic stem cells	blood
40	chr3:69416600-69417400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:69416600-69418400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:69416600-69420400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:69416800-69417200	Enhancers	GM12878-XiMat	blood
44	chr3:69416800-69417400	Enhancers	Primary T cells from cord blood	blood
45	chr3:69416800-69417400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:69416800-69419800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:69416800-69420400	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:69416800-69420600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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