Variant report

Variant	rs11560627
Chromosome Location	chr9:86287401-86287402
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86286368..86289012-chr9:86322464..86325931,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

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

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

rs_ID	r²[population]
rs11140178	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11140179	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140182	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140183	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140191	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140192	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140197	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140199	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140203	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11140215	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11140217	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140219	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140225	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140228	1.00[EUR][1000 genomes]
rs11140229	1.00[EUR][1000 genomes]
rs11140230	0.92[EUR][1000 genomes]
rs11140235	1.00[EUR][1000 genomes]
rs11140248	1.00[EUR][1000 genomes]
rs11140250	1.00[EUR][1000 genomes]
rs11140252	1.00[EUR][1000 genomes]
rs11140254	1.00[EUR][1000 genomes]
rs11140257	1.00[EUR][1000 genomes]
rs11140258	1.00[EUR][1000 genomes]
rs11140266	0.92[EUR][1000 genomes]
rs11140269	0.85[EUR][1000 genomes]
rs11140270	0.85[EUR][1000 genomes]
rs11559387	0.85[EUR][1000 genomes]
rs12235151	0.92[EUR][1000 genomes]
rs12236455	0.92[EUR][1000 genomes]
rs12236743	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12237262	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12237555	1.00[EUR][1000 genomes]
rs12238365	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12238575	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2282221	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2282222	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28627139	1.00[EUR][1000 genomes]
rs28655802	0.86[EUR][1000 genomes]
rs3763626	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr9:86252800-86294000	Weak transcription	Small Intestine	intestine
2	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
4	chr9:86264600-86297000	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr9:86264800-86294600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:86264800-86295600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:86264800-86298200	Strong transcription	Dnd41	blood
8	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:86265000-86295200	Strong transcription	HSMM	muscle
10	chr9:86265000-86296800	Strong transcription	Liver	Liver
11	chr9:86265000-86298800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr9:86266200-86296000	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr9:86266400-86298800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr9:86267000-86292000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:86267000-86293800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr9:86267400-86296800	Strong transcription	A549	lung
17	chr9:86267400-86297800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:86267600-86296800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr9:86267800-86295400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:86268000-86295400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:86268000-86298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:86268200-86294800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:86269000-86294200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:86269200-86289000	Strong transcription	Osteobl	bone
25	chr9:86269200-86297800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:86269400-86298600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:86270400-86295400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:86270800-86298000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr9:86271200-86298000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:86272800-86294000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:86273600-86298600	Weak transcription	Stomach Mucosa	stomach
32	chr9:86273600-86299000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:86273800-86304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:86274800-86288600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:86276200-86295400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr9:86278800-86290400	Weak transcription	Fetal Heart	heart
37	chr9:86279000-86287600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:86279200-86288800	Weak transcription	Right Ventricle	heart
39	chr9:86279200-86291600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr9:86279200-86292600	Weak transcription	Brain Substantia Nigra	brain
41	chr9:86279200-86292600	Weak transcription	Colonic Mucosa	Colon
42	chr9:86279800-86291800	Weak transcription	Pancreas	Pancrea
43	chr9:86279800-86299200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr9:86280000-86287600	Weak transcription	Lung	lung
45	chr9:86280000-86287800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:86280000-86288600	Weak transcription	Esophagus	oesophagus
47	chr9:86280000-86291000	Weak transcription	Brain Germinal Matrix	brain
48	chr9:86280200-86287800	Weak transcription	Fetal Intestine Small	intestine
49	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:86281400-86291800	Weak transcription	Brain Cingulate Gyrus	brain

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