Variant report

Variant	rs12052836
Chromosome Location	chr2:98565144-98565145
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98560596..98562974-chr2:98563175..98565676,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10432626	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11678591	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11679828	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11680018	0.83[EUR][1000 genomes]
rs11680321	0.81[ASN][1000 genomes]
rs11680883	0.84[EUR][1000 genomes]
rs11681535	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11684749	0.82[ASN][1000 genomes]
rs11688829	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11690687	0.84[EUR][1000 genomes]
rs11690737	0.84[EUR][1000 genomes]
rs11691494	0.82[ASN][1000 genomes]
rs11692010	0.82[ASN][1000 genomes]
rs11692470	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12052222	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12052846	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12104810	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13008968	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13020776	0.81[ASN][1000 genomes]
rs13023980	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13028954	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13032265	0.82[ASN][1000 genomes]
rs13032883	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17489454	0.82[ASN][1000 genomes]
rs17489915	0.82[ASN][1000 genomes]
rs17490429	0.82[EUR][1000 genomes]
rs1838797	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1875699	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2044458	0.81[ASN][1000 genomes]
rs2044459	0.82[EUR][1000 genomes]
rs2084176	0.82[EUR][1000 genomes]
rs2278700	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305143	0.82[ASN][1000 genomes]
rs2871183	0.82[ASN][1000 genomes]
rs3198055	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34373359	0.82[EUR][1000 genomes]
rs34502870	0.82[ASN][1000 genomes]
rs34503448	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34528940	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34974566	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35098301	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35218942	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35255677	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35424768	0.82[ASN][1000 genomes]
rs35505530	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35564270	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35783535	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4311104	0.82[ASN][1000 genomes]
rs55886305	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57681139	0.81[ASN][1000 genomes]
rs58546246	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62156511	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6710088	0.83[AMR][1000 genomes]
rs6711101	0.81[ASN][1000 genomes]
rs6746768	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6748124	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6757357	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7421146	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7564773	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7583868	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601898	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs953320	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

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	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv960975	chr2:98562321-98567447	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98553200-98565800	Weak transcription	Small Intestine	intestine
2	chr2:98553800-98565800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:98554000-98565800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:98554000-98570200	Weak transcription	Primary B cells from cord blood	blood
5	chr2:98554400-98565400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr2:98559800-98567800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:98560200-98566400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:98561400-98566800	Weak transcription	HSMMtube	muscle
9	chr2:98561800-98565800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:98561800-98566800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:98561800-98570200	Weak transcription	Primary T cells from cord blood	blood
12	chr2:98562000-98567400	Weak transcription	Brain Substantia Nigra	brain
13	chr2:98562200-98566200	Weak transcription	HSMM	muscle
14	chr2:98562200-98570400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr2:98562400-98569200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:98562600-98565400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:98562600-98565600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:98562600-98565600	Weak transcription	HMEC	breast
19	chr2:98562600-98566400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:98562600-98566400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:98562600-98566400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:98562600-98566400	Weak transcription	NHDF-Ad	bronchial
23	chr2:98562600-98566400	Weak transcription	Osteobl	bone
24	chr2:98562600-98566600	Weak transcription	NHEK	skin
25	chr2:98562600-98566800	Weak transcription	Right Ventricle	heart
26	chr2:98562600-98566800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:98562600-98567200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:98562600-98567600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:98562600-98567800	Weak transcription	Liver	Liver
30	chr2:98562600-98568000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr2:98562600-98570000	Weak transcription	Fetal Intestine Small	intestine
32	chr2:98562600-98570200	Weak transcription	Fetal Lung	lung
33	chr2:98562800-98567800	Weak transcription	Right Atrium	heart
34	chr2:98563000-98565800	Weak transcription	NHLF	lung
35	chr2:98563000-98566800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:98563200-98565800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:98563200-98567000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:98563200-98567200	Weak transcription	Stomach Mucosa	stomach
39	chr2:98563400-98570600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:98563600-98566800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:98563600-98569600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:98564400-98566000	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:98564400-98566200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:98564600-98567400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:98564600-98567600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:98564600-98580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:98564800-98565200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr2:98565000-98566200	Enhancers	Primary monocytes fromperipheralblood	blood

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