Variant report

Variant	rs10116656
Chromosome Location	chr9:108137525-108137526
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	chr9:108006618..108008431-chr9:108135887..108137771,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10081709	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10115833	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10115879	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10120853	0.81[AMR][1000 genomes]
rs10991635	0.81[AMR][1000 genomes]
rs11506819	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339205	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12348983	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13289885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13297419	1.00[EUR][1000 genomes]
rs13298325	1.00[EUR][1000 genomes]
rs13299711	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16924487	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16924552	0.97[AFR][1000 genomes]
rs2417642	0.98[AFR][1000 genomes]
rs28409512	0.93[AFR][1000 genomes]
rs28545469	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34253461	1.00[EUR][1000 genomes]
rs34350840	1.00[EUR][1000 genomes]
rs34999484	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs35111325	1.00[EUR][1000 genomes]
rs35275407	1.00[EUR][1000 genomes]
rs35322610	1.00[EUR][1000 genomes]
rs35533765	1.00[EUR][1000 genomes]
rs4538947	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60502553	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479309	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479317	0.98[AFR][1000 genomes]
rs67844420	1.00[EUR][1000 genomes]
rs7019220	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7031117	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7034136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7034666	0.81[AMR][1000 genomes]
rs7040751	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71494522	0.88[EUR][1000 genomes]
rs71494524	1.00[EUR][1000 genomes]
rs71494526	1.00[EUR][1000 genomes]
rs71494527	1.00[EUR][1000 genomes]
rs7856033	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7856524	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7860321	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7870687	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7871855	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299385	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299386	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299387	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9632901	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
4	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
5	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:108097600-108147000	Weak transcription	HMEC	breast
7	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
8	chr9:108104800-108147600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:108105000-108149600	Weak transcription	Right Ventricle	heart
10	chr9:108105000-108151200	Weak transcription	Gastric	stomach
11	chr9:108105000-108154800	Weak transcription	Small Intestine	intestine
12	chr9:108105200-108149800	Weak transcription	NHDF-Ad	bronchial
13	chr9:108117000-108146400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr9:108117400-108147400	Weak transcription	Spleen	Spleen
15	chr9:108118200-108147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:108118400-108139800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:108118600-108147600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr9:108120200-108146200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:108121400-108139400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:108121600-108157000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:108121800-108148600	Weak transcription	A549	lung
22	chr9:108122400-108148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr9:108122600-108153400	Weak transcription	Stomach Mucosa	stomach
24	chr9:108123600-108154400	Weak transcription	Colonic Mucosa	Colon
25	chr9:108123800-108147600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:108124200-108147000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr9:108124200-108147600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:108124400-108147400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr9:108124400-108151000	Weak transcription	Fetal Brain Male	brain
30	chr9:108124600-108151800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:108125000-108166800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr9:108125200-108147000	Weak transcription	GM12878-XiMat	blood
33	chr9:108125400-108147000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:108125400-108147600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr9:108125400-108149800	Weak transcription	HSMMtube	muscle
36	chr9:108125600-108157000	Weak transcription	Osteobl	bone
37	chr9:108126000-108152000	Weak transcription	Brain Germinal Matrix	brain
38	chr9:108126400-108137600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:108126400-108147800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:108127000-108147800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr9:108127200-108151800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:108128200-108151400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr9:108130200-108147800	Weak transcription	Ovary	ovary
44	chr9:108130600-108146600	Weak transcription	Hela-S3	cervix
45	chr9:108130800-108147600	Weak transcription	Primary B cells from cord blood	blood
46	chr9:108132200-108145400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:108132400-108147000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:108134400-108146800	Weak transcription	Dnd41	blood
49	chr9:108135000-108147600	Weak transcription	Thymus	Thymus
50	chr9:108135400-108139800	Strong transcription	Fetal Intestine Large	intestine

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