Variant report

Variant	rs10899392
Chromosome Location	chr11:77302378-77302379
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:77300746..77302485-chr11:77346924..77348816,2	MCF-7	breast:
2	chr11:77299407..77303220-chr11:77304055..77306866,3	MCF-7	breast:
3	chr11:77299067..77304108-chr11:77304115..77308042,7	K562	blood:

Variant related genes	Relation type
ENSG00000074201	Chromatin interaction
ENSG00000271767	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10899390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237240	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11237260	0.85[CHB][hapmap]
rs11237261	0.85[CHB][hapmap]
rs11533286	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12221551	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12225695	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs12576652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17825097	0.85[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1038974	chr11:77284036-77431228	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1041384	chr11:77284558-77419809	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1048892	chr11:77290458-77431228	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS 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	16 gene(s)	inside rSNPs	diseases
9	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv468641	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv555452	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77299800-77302400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr11:77299800-77302400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr11:77300200-77302800	Active TSS	Fetal Intestine Large	intestine
4	chr11:77300200-77303200	Active TSS	Ovary	ovary
5	chr11:77300400-77304000	Active TSS	Fetal Intestine Small	intestine
6	chr11:77301400-77308000	Weak transcription	Hela-S3	cervix
7	chr11:77301400-77346000	Weak transcription	Small Intestine	intestine
8	chr11:77301600-77305200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:77301600-77312600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:77301600-77312800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:77301600-77312800	Weak transcription	HMEC	breast
12	chr11:77301600-77313400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:77301600-77317200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:77301600-77317800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr11:77301600-77318600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:77301600-77332800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:77301800-77303000	Active TSS	Duodenum Mucosa	Duodenum
18	chr11:77301800-77303000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr11:77301800-77306800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:77301800-77312400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:77301800-77312800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:77301800-77313000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:77301800-77313800	Weak transcription	Left Ventricle	heart
24	chr11:77301800-77316200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr11:77301800-77316600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:77301800-77317200	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:77301800-77318200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr11:77301800-77322400	Weak transcription	Primary B cells from peripheral blood	blood
29	chr11:77301800-77326600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:77301800-77332200	Weak transcription	Esophagus	oesophagus
31	chr11:77301800-77345800	Weak transcription	Spleen	Spleen
32	chr11:77302000-77302400	Weak transcription	Brain Angular Gyrus	brain
33	chr11:77302000-77302400	Active TSS	HepG2	liver
34	chr11:77302000-77302600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:77302000-77302600	Weak transcription	Fetal Brain Male	brain
36	chr11:77302000-77302800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr11:77302000-77302800	Weak transcription	Pancreas	Pancrea
38	chr11:77302000-77303000	Weak transcription	Stomach Mucosa	stomach
39	chr11:77302000-77307600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:77302000-77308400	Weak transcription	Placenta	Placenta
41	chr11:77302000-77312200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:77302000-77312400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:77302000-77312600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:77302000-77312600	Weak transcription	Brain Substantia Nigra	brain
45	chr11:77302000-77312600	Weak transcription	HSMM	muscle
46	chr11:77302000-77312600	Weak transcription	NHEK	skin
47	chr11:77302000-77312800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:77302000-77312800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:77302000-77312800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:77302000-77312800	Weak transcription	K562	blood

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