Variant report

Variant	rs660686
Chromosome Location	chr9:15297587-15297588
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	chr9:15293831..15297894-chr9:15305171..15308300,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10120504	1.00[JPT][hapmap]
rs10122040	1.00[JPT][hapmap]
rs10122202	1.00[JPT][hapmap]
rs10125329	1.00[JPT][hapmap]
rs10810369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10961950	1.00[JPT][hapmap]
rs10961951	1.00[JPT][hapmap]
rs10961955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10962043	1.00[CHB][hapmap]
rs12003180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1215112	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475229	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2156109	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2185938	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2616751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3901749	1.00[JPT][hapmap]
rs3933784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3933785	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4237138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs471364	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs486349	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs540885	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs570524	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578194	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs581080	0.89[CEU][hapmap]
rs612183	0.82[JPT][hapmap]
rs643531	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs661048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs677578	0.92[ASN][1000 genomes]
rs686030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7873299	0.82[JPT][hapmap]
rs9657588	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv613650	chr9:15296119-15378449	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv613651	chr9:15296355-15358157	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1015960	chr9:15296783-15380657	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:15294400-15306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:15294600-15297600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:15294800-15297600	Enhancers	Lung	lung
8	chr9:15295200-15297800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr9:15295800-15297600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr9:15295800-15298400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr9:15296600-15297600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:15296600-15297600	Enhancers	Fetal Muscle Leg	muscle
13	chr9:15296600-15299000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:15296600-15299400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:15296600-15301200	Enhancers	Primary B cells from peripheral blood	blood
16	chr9:15296800-15297600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:15296800-15297600	Flanking Active TSS	Liver	Liver
18	chr9:15296800-15297600	Enhancers	Fetal Lung	lung
19	chr9:15296800-15297600	Enhancers	Fetal Muscle Trunk	muscle
20	chr9:15296800-15297600	Genic enhancers	Fetal Stomach	stomach
21	chr9:15296800-15297600	Enhancers	Gastric	stomach
22	chr9:15296800-15297600	Enhancers	Stomach Mucosa	stomach
23	chr9:15296800-15297800	Enhancers	Aorta	Aorta
24	chr9:15296800-15297800	Genic enhancers	Fetal Intestine Large	intestine
25	chr9:15296800-15298000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr9:15296800-15298000	Genic enhancers	Fetal Intestine Small	intestine
27	chr9:15296800-15299000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:15296800-15299000	Enhancers	Fetal Thymus	thymus
29	chr9:15296800-15305600	Weak transcription	Left Ventricle	heart
30	chr9:15297000-15297600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
31	chr9:15297000-15297600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:15297000-15297600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:15297000-15297600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr9:15297000-15297600	Enhancers	Right Atrium	heart
35	chr9:15297000-15297600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
36	chr9:15297000-15297600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr9:15297000-15297600	Enhancers	Thymus	Thymus
38	chr9:15297000-15297600	Enhancers	HMEC	breast
39	chr9:15297000-15297600	Enhancers	Osteobl	bone
40	chr9:15297000-15299000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:15297000-15299400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr9:15297000-15299600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:15297000-15305200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr9:15297200-15297600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr9:15297200-15297600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:15297200-15297600	Enhancers	Esophagus	oesophagus
47	chr9:15297200-15297600	Enhancers	Fetal Kidney	kidney
48	chr9:15297200-15297600	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr9:15297200-15297600	Enhancers	Pancreas	Pancrea
50	chr9:15297200-15297600	Enhancers	Rectal Mucosa Donor 29	rectum

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