Variant report

Variant	rs7858899
Chromosome Location	chr9:19062353-19062354
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	chr9:19047815..19051920-chr9:19059241..19062627,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10116604	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10117419	0.87[ASN][1000 genomes]
rs10117445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10119748	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10811070	1.00[CHB][hapmap]
rs10811115	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10963853	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963856	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963858	1.00[CHB][hapmap]
rs10963860	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963861	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963868	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963883	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963888	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963889	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963890	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10963918	1.00[CHB][hapmap]
rs10963937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963945	0.85[EUR][1000 genomes]
rs10963959	0.82[EUR][1000 genomes]
rs11496354	0.83[AMR][1000 genomes]
rs12115446	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12346001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12379525	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16937210	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs16937322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs17236157	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2039007	1.00[CHB][hapmap]
rs2233800	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3177673	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4478656	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7031878	1.00[CHB][hapmap]
rs7031911	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7848851	1.00[JPT][hapmap]
rs883440	1.00[CEU][hapmap];1.00[CHB][hapmap]

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	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:19050800-19074200	Weak transcription	Lung	lung
5	chr9:19051400-19066400	Weak transcription	Colonic Mucosa	Colon
6	chr9:19051600-19074400	Weak transcription	Spleen	Spleen
7	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:19051800-19070200	Weak transcription	Fetal Kidney	kidney
9	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:19052000-19062600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:19052000-19075200	Weak transcription	Right Ventricle	heart
12	chr9:19052400-19077000	Weak transcription	Pancreas	Pancrea
13	chr9:19052600-19065000	Weak transcription	Small Intestine	intestine
14	chr9:19052800-19062600	Weak transcription	Brain Angular Gyrus	brain
15	chr9:19052800-19074400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:19052800-19075600	Weak transcription	Aorta	Aorta
17	chr9:19052800-19092400	Weak transcription	Fetal Brain Male	brain
18	chr9:19053600-19065000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:19055000-19072600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:19055200-19065600	Strong transcription	Placenta	Placenta
24	chr9:19055400-19065600	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr9:19055400-19065600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:19055600-19082600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr9:19055800-19065400	Strong transcription	Dnd41	blood
29	chr9:19055800-19065400	Strong transcription	HUVEC	blood vessel
30	chr9:19055800-19079800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:19055800-19085200	Strong transcription	Liver	Liver
32	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:19056000-19086000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:19056200-19063000	Strong transcription	Osteobl	bone
39	chr9:19056200-19065600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:19056400-19065400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr9:19056400-19073600	Strong transcription	Hela-S3	cervix
42	chr9:19056600-19062800	Strong transcription	NHDF-Ad	bronchial
43	chr9:19056600-19063000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:19056600-19063000	Strong transcription	HepG2	liver
45	chr9:19056600-19063200	Strong transcription	Left Ventricle	heart
46	chr9:19056600-19064000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr9:19056600-19064000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:19056600-19064000	Strong transcription	Fetal Intestine Large	intestine
49	chr9:19056600-19064200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr9:19056600-19065400	Strong transcription	Duodenum Mucosa	Duodenum

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