Variant report

Variant	rs12223658
Chromosome Location	chr11:65779961-65779962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65624802..65627661-chr11:65779805..65782359,2	MCF-7	breast:
2	chr11:65778738..65782540-chr11:65791690..65794306,3	MCF-7	breast:
3	chr11:65727748..65729468-chr11:65777688..65780268,2	MCF-7	breast:
4	chr11:65684023..65687163-chr11:65778751..65782457,4	MCF-7	breast:
5	chr11:65624293..65627593-chr11:65778197..65781174,3	MCF-7	breast:
6	chr11:65188418..65191702-chr11:65777424..65780862,3	MCF-7	breast:
7	chr11:65778958..65780961-chr11:65818944..65820828,4	MCF-7	breast:
8	chr11:65650838..65654244-chr11:65778689..65782514,4	MCF-7	breast:
9	chr11:65779081..65782393-chr11:65836476..65839425,3	MCF-7	breast:
10	chr11:65655400..65657605-chr11:65778805..65780715,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175467	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000238752	Chromatin interaction
ENSG00000172732	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10896069	0.91[ASN][1000 genomes]
rs11227352	0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11227357	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11227358	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11227361	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11227363	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11227369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11227380	1.00[AMR][1000 genomes]
rs11227394	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs1151513	0.89[ASN][1000 genomes]
rs1211380	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12278133	1.00[YRI][hapmap]
rs12286846	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1892901	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2096903	0.94[ASN][1000 genomes]
rs2847698	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3741372	1.00[AMR][1000 genomes]
rs3814747	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs3814748	0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs4930165	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4930327	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4930329	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4930331	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7103709	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7125150	0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs744478	0.82[JPT][hapmap]
rs7937692	0.82[JPT][hapmap];1.00[MEX][hapmap]
rs9666934	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
6	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65773400-65780200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr11:65774800-65780200	Weak transcription	Hela-S3	cervix
3	chr11:65775600-65780200	Weak transcription	K562	blood
4	chr11:65776800-65780600	Weak transcription	A549	lung
5	chr11:65776800-65781400	Weak transcription	HSMMtube	muscle
6	chr11:65777000-65780600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:65778000-65781000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr11:65778200-65781000	Enhancers	HMEC	breast
9	chr11:65778200-65781600	Enhancers	Placenta	Placenta
10	chr11:65778800-65780000	Enhancers	HSMM	muscle
11	chr11:65778800-65781200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:65778800-65781200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:65779000-65780000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr11:65779000-65780000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:65779000-65780000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:65779000-65780400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
17	chr11:65779000-65780400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:65779000-65780400	Active TSS	Esophagus	oesophagus
19	chr11:65779000-65780600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr11:65779000-65781000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr11:65779000-65781200	Bivalent Enhancer	Fetal Thymus	thymus
22	chr11:65779200-65780000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
23	chr11:65779200-65780200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
24	chr11:65779200-65780600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
25	chr11:65779200-65782400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:65779400-65780000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr11:65779400-65780000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
28	chr11:65779400-65780000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
29	chr11:65779400-65780200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:65779400-65780200	Weak transcription	Aorta	Aorta
31	chr11:65779400-65780200	Weak transcription	HUVEC	blood vessel
32	chr11:65779400-65780400	Enhancers	Spleen	Spleen
33	chr11:65779400-65780600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:65779400-65780600	Enhancers	Primary hematopoietic stem cells	blood
35	chr11:65779400-65781000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr11:65779600-65780000	Bivalent Enhancer	Colon Smooth Muscle	Colon
37	chr11:65779600-65780000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
38	chr11:65779600-65780200	Weak transcription	Osteobl	bone
39	chr11:65779600-65780400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:65779600-65780800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
41	chr11:65779600-65782600	Weak transcription	Lung	lung
42	chr11:65779800-65780000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:65779800-65780000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:65779800-65780000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
45	chr11:65779800-65780000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr11:65779800-65780000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
47	chr11:65779800-65780000	Bivalent Enhancer	NHEK	skin
48	chr11:65779800-65780200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
49	chr11:65779800-65780400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:65779800-65780400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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