Variant report

Variant	rs11189096
Chromosome Location	chr10:99044073-99044074
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	chr10:99043100..99045603-chr10:99092696..99094572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181274	Chromatin interaction
ENSG00000225850	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10509713	0.93[AMR][1000 genomes]
rs11189064	0.87[AMR][1000 genomes]
rs11189065	0.87[AMR][1000 genomes]
rs11189066	0.87[AMR][1000 genomes]
rs11189067	0.87[AMR][1000 genomes]
rs11189072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189080	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189081	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189086	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11189087	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11189090	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189092	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189093	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11189094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189095	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11189097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189098	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11189106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189107	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11189117	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189118	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189125	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189129	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11189136	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11189140	0.87[AMR][1000 genomes]
rs11189141	0.87[AMR][1000 genomes]
rs11189143	0.87[AMR][1000 genomes]
rs11189145	0.93[AMR][1000 genomes]
rs11189146	0.93[AMR][1000 genomes]
rs11189148	0.93[AMR][1000 genomes]
rs11189149	0.93[AMR][1000 genomes]
rs11189158	0.93[AMR][1000 genomes]
rs11189162	0.87[AMR][1000 genomes]
rs11189166	0.93[AMR][1000 genomes]
rs11189170	0.93[AMR][1000 genomes]
rs12355279	0.93[AMR][1000 genomes]
rs12355311	0.87[AMR][1000 genomes]
rs12355523	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12355526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356909	0.87[AMR][1000 genomes]
rs12358104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12358257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12358267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12358452	0.87[AMR][1000 genomes]
rs12358777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12359143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12359467	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12359643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12359654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12360528	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1414742	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1810982	0.87[AMR][1000 genomes]
rs1970191	0.93[AMR][1000 genomes]
rs1970454	0.93[AMR][1000 genomes]
rs41284270	0.93[AMR][1000 genomes]
rs45527941	0.93[AMR][1000 genomes]
rs7917149	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs884450	0.93[AMR][1000 genomes]
rs9645543	0.87[AMR][1000 genomes]
rs9645559	0.87[AMR][1000 genomes]
rs9645560	0.87[AMR][1000 genomes]
rs9645561	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1040903	chr10:98986382-99047475	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv7507	chr10:99031233-99070690	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98978600-99051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:98987200-99051200	Weak transcription	Pancreas	Pancrea
3	chr10:99005200-99046800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr10:99019400-99050000	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr10:99019400-99051600	Weak transcription	Ovary	ovary
6	chr10:99021400-99051000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:99023600-99051200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr10:99024000-99046800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr10:99024000-99050800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr10:99024400-99050000	Weak transcription	Spleen	Spleen
11	chr10:99024800-99051200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:99025800-99050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr10:99026000-99051200	Weak transcription	Primary T cells from cord blood	blood
14	chr10:99027600-99046200	Weak transcription	Thymus	Thymus
15	chr10:99027800-99045600	Weak transcription	Fetal Thymus	thymus
16	chr10:99028600-99051200	Weak transcription	Small Intestine	intestine
17	chr10:99028800-99046800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr10:99031400-99050400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr10:99034800-99046600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr10:99038000-99046800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:99038000-99050400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr10:99038600-99046800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr10:99038800-99046400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr10:99038800-99046400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr10:99038800-99046800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:99038800-99047200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr10:99038800-99051200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr10:99038800-99051200	Weak transcription	Brain Germinal Matrix	brain
29	chr10:99038800-99051200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:99038800-99051200	Weak transcription	NH-A	brain
31	chr10:99038800-99051400	Weak transcription	Brain Angular Gyrus	brain
32	chr10:99039000-99045600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr10:99039000-99046000	Weak transcription	Fetal Stomach	stomach
34	chr10:99039000-99046800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr10:99039000-99050600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr10:99039000-99050800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr10:99039000-99051200	Weak transcription	Colon Smooth Muscle	Colon
38	chr10:99039000-99051200	Weak transcription	HUVEC	blood vessel
39	chr10:99039000-99051400	Weak transcription	Brain Anterior Caudate	brain
40	chr10:99039200-99045600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr10:99039400-99046600	Weak transcription	Fetal Lung	lung
42	chr10:99039400-99046800	Weak transcription	Fetal Kidney	kidney
43	chr10:99039400-99051200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:99039400-99051200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr10:99039400-99051200	Weak transcription	NHEK	skin
46	chr10:99039400-99051400	Weak transcription	Adipose Nuclei	Adipose
47	chr10:99039600-99045800	Weak transcription	Dnd41	blood
48	chr10:99039600-99046200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr10:99039600-99046600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr10:99039600-99046600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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