Variant report

Variant	rs12099125
Chromosome Location	chr11:65680010-65680011
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65623382..65625608-chr11:65679058..65681243,2	MCF-7	breast:
2	chr11:65679333..65681009-chr11:65720211..65722785,2	MCF-7	breast:
3	chr11:65650579..65663306-chr11:65677153..65690311,39	MCF-7	breast:
4	chr11:65655648..65656257-chr11:65679363..65680211,2	MCF-7	breast:
5	chr11:65622510..65630779-chr11:65675126..65689187,23	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172757	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000172732	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10791831	1.00[ASN][1000 genomes]
rs10896065	0.97[ASN][1000 genomes]
rs11227338	0.96[ASN][1000 genomes]
rs11542177	1.00[ASN][1000 genomes]
rs12099359	1.00[ASN][1000 genomes]
rs12575514	0.81[ASN][1000 genomes]
rs12576224	0.94[ASN][1000 genomes]
rs12576319	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12577625	0.81[ASN][1000 genomes]
rs28372938	0.81[ASN][1000 genomes]
rs58192075	1.00[ASN][1000 genomes]
rs58905199	0.81[ASN][1000 genomes]
rs61515492	0.86[ASN][1000 genomes]
rs653955	1.00[ASN][1000 genomes]
rs67232706	0.83[ASN][1000 genomes]
rs67530871	0.83[ASN][1000 genomes]
rs72928828	0.81[ASN][1000 genomes]
rs72928830	0.81[ASN][1000 genomes]
rs73496412	1.00[ASN][1000 genomes]
rs73496423	0.97[ASN][1000 genomes]
rs73496424	1.00[ASN][1000 genomes]
rs73496435	1.00[ASN][1000 genomes]
rs7927841	0.89[ASN][1000 genomes]
rs7940700	0.97[ASN][1000 genomes]
rs7941052	0.94[ASN][1000 genomes]
rs9326357	0.84[ASN][1000 genomes]
rs9326362	0.94[ASN][1000 genomes]
rs9919533	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
3	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
6	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65668000-65682600	Weak transcription	Aorta	Aorta
2	chr11:65676400-65683600	Enhancers	NHDF-Ad	bronchial
3	chr11:65676400-65683800	Weak transcription	Primary T cells from cord blood	blood
4	chr11:65677000-65682200	Weak transcription	Pancreas	Pancrea
5	chr11:65677000-65682400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:65677200-65681600	Enhancers	GM12878-XiMat	blood
7	chr11:65677600-65682200	Enhancers	NHLF	lung
8	chr11:65677600-65682800	Enhancers	A549	lung
9	chr11:65677800-65684000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:65678000-65681600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:65678000-65682800	Enhancers	HMEC	breast
12	chr11:65678600-65680400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr11:65678600-65680800	Enhancers	HUVEC	blood vessel
14	chr11:65678600-65681000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:65678600-65681400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:65678600-65681600	Enhancers	NH-A	brain
17	chr11:65678800-65680200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr11:65678800-65680200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:65678800-65680400	Enhancers	Fetal Stomach	stomach
20	chr11:65678800-65680600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr11:65678800-65680800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:65678800-65681000	Enhancers	Adipose Nuclei	Adipose
23	chr11:65678800-65681200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:65678800-65681600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr11:65679000-65680600	Enhancers	Stomach Mucosa	stomach
26	chr11:65679000-65680800	Enhancers	K562	blood
27	chr11:65679000-65680800	Flanking Active TSS	NHEK	skin
28	chr11:65679000-65681600	Enhancers	Esophagus	oesophagus
29	chr11:65679200-65681000	Enhancers	Fetal Thymus	thymus
30	chr11:65679200-65681200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr11:65679400-65682200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:65679400-65682400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:65679400-65682400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:65679400-65682600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:65679400-65685200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:65679600-65680400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr11:65679600-65681000	Enhancers	Fetal Muscle Leg	muscle
38	chr11:65679600-65681200	Enhancers	Fetal Muscle Trunk	muscle
39	chr11:65679600-65681600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr11:65679600-65682200	Weak transcription	Psoas Muscle	Psoas
41	chr11:65679600-65682200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr11:65679600-65682400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:65679600-65682400	Weak transcription	Lung	lung
44	chr11:65679600-65682400	Weak transcription	Right Atrium	heart
45	chr11:65679600-65682400	Weak transcription	Spleen	Spleen
46	chr11:65679600-65682600	Weak transcription	Fetal Intestine Small	intestine
47	chr11:65679600-65682800	Weak transcription	Brain Germinal Matrix	brain
48	chr11:65679600-65682800	Enhancers	Osteobl	bone
49	chr11:65679600-65683200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:65679600-65683200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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