Variant report

Variant	rs17011966
Chromosome Location	chr4:87556253-87556254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10516775	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10516776	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1344260	0.87[EUR][1000 genomes]
rs17011953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011954	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011956	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011959	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011962	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011965	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011968	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011978	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011981	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011984	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011985	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011988	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011994	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012007	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012009	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012010	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012012	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012018	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17419783	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17454077	0.82[CEU][hapmap]
rs17454369	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2170427	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2200052	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2219993	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648374	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28653505	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2869442	0.87[EUR][1000 genomes]
rs2869443	0.87[EUR][1000 genomes]
rs2904103	0.87[EUR][1000 genomes]
rs34155193	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35434858	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4561893	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4604024	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4627823	0.87[EUR][1000 genomes]
rs61121590	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61344492	0.87[EUR][1000 genomes]
rs72870675	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72872208	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72872209	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7690137	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs980637	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980638	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv879523	chr4:87517609-87594472	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv879524	chr4:87517609-87603929	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv2755470	chr4:87536515-87613212	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87541200-87571200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:87542800-87557600	Weak transcription	Brain Anterior Caudate	brain
3	chr4:87542800-87566400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:87543200-87556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr4:87544400-87556800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:87544400-87571200	Weak transcription	Pancreas	Pancrea
7	chr4:87546200-87569400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:87546400-87556400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:87546400-87557000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:87551400-87556800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:87552200-87556400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:87552600-87556800	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:87552800-87557800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87553400-87557800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:87553600-87556400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:87554600-87557000	Weak transcription	HMEC	breast
17	chr4:87554600-87558800	Weak transcription	Lung	lung
18	chr4:87554600-87567000	Weak transcription	Osteobl	bone
19	chr4:87554600-87567400	Weak transcription	Esophagus	oesophagus
20	chr4:87554800-87566000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:87555000-87557200	Weak transcription	Brain Substantia Nigra	brain
22	chr4:87555000-87558800	Weak transcription	Brain Germinal Matrix	brain
23	chr4:87555200-87556800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:87555200-87559400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:87555400-87556600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:87555400-87557000	Weak transcription	Fetal Lung	lung
27	chr4:87555400-87557200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:87555600-87557800	Strong transcription	NHDF-Ad	bronchial
29	chr4:87555800-87557600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr4:87555800-87557800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:87555800-87557800	Strong transcription	NHEK	skin
32	chr4:87555800-87558000	Weak transcription	NHLF	lung
33	chr4:87555800-87567600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:87555800-87567800	Weak transcription	Fetal Intestine Large	intestine
35	chr4:87556000-87556600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:87556000-87557200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:87556000-87557200	Weak transcription	Fetal Kidney	kidney
38	chr4:87556000-87557400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:87556000-87557400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:87556000-87557600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:87556000-87557800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:87556000-87557800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:87556000-87557800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:87556000-87558000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr4:87556000-87558600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:87556200-87556400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr4:87556200-87556600	Genic enhancers	Ovary	ovary
48	chr4:87556200-87557200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:87556200-87557600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr4:87556200-87557600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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