Variant report

Variant	rs16959834
Chromosome Location	chr17:16471690-16471691
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	chr17:16470312..16472468-chr17:16555648..16557862,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264765	Chromatin interaction
ENSG00000197566	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs16959831	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs16959832	0.91[ASW][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs6502509	0.91[ASW][hapmap]
rs7211497	0.91[ASW][hapmap];0.85[YRI][hapmap]
rs7212777	0.85[YRI][hapmap]
rs7218177	0.84[AFR][1000 genomes]
rs7220867	0.82[AFR][1000 genomes]
rs73980200	0.81[AFR][1000 genomes]
rs8069772	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs8069951	0.84[AFR][1000 genomes]
rs9899370	0.85[YRI][hapmap]
rs9908067	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
6	nsv1061463	chr17:16245878-16490691	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
7	nsv543216	chr17:16245878-16490691	Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	99 gene(s)	inside rSNPs	diseases
8	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16459600-16471800	Weak transcription	Stomach Mucosa	stomach
2	chr17:16461200-16471800	Weak transcription	Gastric	stomach
3	chr17:16462200-16471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:16462200-16471800	Weak transcription	Esophagus	oesophagus
5	chr17:16462200-16471800	Weak transcription	Pancreas	Pancrea
6	chr17:16464600-16471800	Weak transcription	Lung	lung
7	chr17:16467000-16471800	Weak transcription	Colonic Mucosa	Colon
8	chr17:16467600-16471800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr17:16467800-16471800	Weak transcription	Ovary	ovary
10	chr17:16468000-16471800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:16468400-16471800	Weak transcription	Aorta	Aorta
12	chr17:16469600-16471800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr17:16469800-16471800	ZNF genes & repeats	A549	lung
14	chr17:16470600-16471800	Weak transcription	Left Ventricle	heart
15	chr17:16470800-16471800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:16471000-16471800	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr17:16471000-16471800	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr17:16471000-16471800	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr17:16471000-16471800	Flanking Active TSS	Fetal Brain Female	brain
20	chr17:16471000-16472000	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr17:16471200-16471800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr17:16471200-16471800	Enhancers	Fetal Lung	lung
23	chr17:16471200-16471800	Enhancers	Rectal Smooth Muscle	rectum
24	chr17:16471200-16472000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr17:16471200-16472600	Active TSS	Fetal Kidney	kidney
26	chr17:16471200-16472800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:16471200-16472800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:16471200-16473000	Flanking Active TSS	Dnd41	blood
29	chr17:16471400-16471800	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr17:16471400-16471800	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr17:16471400-16472000	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr17:16471400-16472000	Flanking Active TSS	Fetal Brain Male	brain
33	chr17:16471400-16472200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:16471600-16471800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr17:16471600-16471800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr17:16471600-16471800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:16471600-16471800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr17:16471600-16471800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:16471600-16471800	Enhancers	Primary B cells from cord blood	blood
40	chr17:16471600-16471800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr17:16471600-16471800	Enhancers	Primary hematopoietic stem cells	blood
42	chr17:16471600-16471800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr17:16471600-16471800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:16471600-16471800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:16471600-16471800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr17:16471600-16471800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr17:16471600-16471800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr17:16471600-16471800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr17:16471600-16471800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:16471600-16471800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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