Variant report

Variant	rs17454369
Chromosome Location	chr4:87666334-87666335
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10516775	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10516776	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011954	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011956	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011962	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011966	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011968	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011978	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011981	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011984	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011985	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011988	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17011994	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17012007	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17419783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17454077	1.00[AFR][1000 genomes]
rs2170427	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2200052	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2219993	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28653505	0.83[AMR][1000 genomes];0.97[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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4604024	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61121590	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72870675	0.83[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]
rs980637	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs980638	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9991627	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv508296	chr4:87636350-87667372	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
2	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
3	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
5	chr4:87639400-87739200	Weak transcription	A549	lung
6	chr4:87641800-87683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:87642200-87692600	Weak transcription	NH-A	brain
8	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:87642600-87692400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:87642600-87697600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:87642600-87719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:87644600-87680600	Weak transcription	NHLF	lung
13	chr4:87650400-87677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87651800-87676400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:87652600-87670000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:87655600-87704400	Weak transcription	Hela-S3	cervix
17	chr4:87659000-87676400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:87661600-87671600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:87661600-87671600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:87661600-87680400	Weak transcription	Brain Substantia Nigra	brain
21	chr4:87661600-87680600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:87661600-87683200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:87661600-87710200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:87661600-87711400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:87661600-87712000	Weak transcription	Esophagus	oesophagus
26	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:87661800-87670400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:87661800-87671400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:87661800-87671600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:87661800-87671600	Weak transcription	Lung	lung
31	chr4:87661800-87676600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:87661800-87683000	Weak transcription	Fetal Stomach	stomach
33	chr4:87661800-87683200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:87661800-87683800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:87661800-87708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:87661800-87712000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
38	chr4:87662000-87669000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr4:87662000-87669200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:87662000-87675600	Weak transcription	Gastric	stomach
41	chr4:87662400-87669600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:87663000-87672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr4:87663000-87683600	Weak transcription	Fetal Brain Female	brain
44	chr4:87663000-87711400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:87663400-87675400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:87664000-87670800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:87664400-87667800	Strong transcription	HMEC	breast
48	chr4:87664800-87667200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr4:87665000-87692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:87665200-87666600	Strong transcription	Fetal Kidney	kidney

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