Variant report

Variant	rs16959831
Chromosome Location	chr17:16470134-16470135
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	chr17:16468870..16470637-chr17:16474306..16477417,3	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1006561	1.00[EUR][1000 genomes]
rs16959784	1.00[EUR][1000 genomes]
rs16959821	0.83[AFR][1000 genomes]
rs16959832	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16959834	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs16959849	1.00[EUR][1000 genomes]
rs28375510	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28375681	1.00[EUR][1000 genomes]
rs28481713	1.00[EUR][1000 genomes]
rs28482815	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57062804	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57088651	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57432974	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6502511	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6502512	0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7211497	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7212777	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214389	1.00[EUR][1000 genomes]
rs7218171	1.00[EUR][1000 genomes]
rs7218177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7220797	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7220867	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7221073	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7222107	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73282666	1.00[EUR][1000 genomes]
rs73282673	1.00[EUR][1000 genomes]
rs73282675	1.00[EUR][1000 genomes]
rs73282678	1.00[EUR][1000 genomes]
rs73980200	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8066377	1.00[EUR][1000 genomes]
rs8068846	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069772	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069951	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9890785	1.00[EUR][1000 genomes]
rs9899370	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900136	1.00[EUR][1000 genomes]
rs9900601	1.00[EUR][1000 genomes]
rs9902632	1.00[EUR][1000 genomes]
rs9912467	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912759	1.00[EUR][1000 genomes]
rs9916250	1.00[EUR][1000 genomes]

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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16455000-16471200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:16458800-16471600	Weak transcription	HUVEC	blood vessel
3	chr17:16459600-16471800	Weak transcription	Stomach Mucosa	stomach
4	chr17:16461200-16471800	Weak transcription	Gastric	stomach
5	chr17:16462200-16470800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:16462200-16471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:16462200-16471800	Weak transcription	Esophagus	oesophagus
8	chr17:16462200-16471800	Weak transcription	Pancreas	Pancrea
9	chr17:16463200-16470800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr17:16463200-16471200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr17:16463200-16471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr17:16463400-16470800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:16463400-16471000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:16463400-16471200	Weak transcription	Fetal Kidney	kidney
15	chr17:16463800-16471000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:16464000-16471000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:16464000-16471200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr17:16464400-16470200	Strong transcription	Brain Anterior Caudate	brain
19	chr17:16464400-16471400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:16464600-16471800	Weak transcription	Lung	lung
21	chr17:16465000-16471600	Weak transcription	HMEC	breast
22	chr17:16465200-16471600	Weak transcription	Fetal Heart	heart
23	chr17:16465600-16470600	Strong transcription	Left Ventricle	heart
24	chr17:16466200-16470800	Strong transcription	Fetal Muscle Leg	muscle
25	chr17:16466600-16471000	Strong transcription	Fetal Stomach	stomach
26	chr17:16466600-16471600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:16466800-16471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr17:16466800-16471600	Weak transcription	NHEK	skin
29	chr17:16467000-16471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:16467000-16471600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:16467000-16471800	Weak transcription	Colonic Mucosa	Colon
32	chr17:16467200-16470400	Weak transcription	Fetal Brain Male	brain
33	chr17:16467200-16470600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:16467200-16470600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr17:16467200-16470800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr17:16467200-16471000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:16467200-16471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr17:16467200-16471600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr17:16467200-16471600	Weak transcription	Fetal Intestine Large	intestine
40	chr17:16467200-16471600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr17:16467200-16471600	Weak transcription	Psoas Muscle	Psoas
42	chr17:16467200-16471600	Weak transcription	Small Intestine	intestine
43	chr17:16467400-16470400	Weak transcription	NHLF	lung
44	chr17:16467400-16470600	Weak transcription	Brain Angular Gyrus	brain
45	chr17:16467400-16470600	Weak transcription	Placenta	Placenta
46	chr17:16467400-16471000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr17:16467400-16471200	Weak transcription	Thymus	Thymus
48	chr17:16467400-16471600	Weak transcription	Fetal Thymus	thymus
49	chr17:16467400-16471600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr17:16467400-16471600	Weak transcription	Right Ventricle	heart

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