Variant report

Variant	rs2723828
Chromosome Location	chr12:11929153-11929154
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	chr12:11928703..11930258-chr12:11944667..11947353,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2051523	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2723827	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2723830	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2724594	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2724658	0.87[EUR][1000 genomes]
rs2856327	0.90[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs3741429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782140	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7961094	0.82[EUR][1000 genomes]
rs7967177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870039	chr12:11800363-11996598	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	nsv1053609	chr12:11898099-11933906	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv469113	chr12:11913360-11931259	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv557574	chr12:11913360-11931259	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv469114	chr12:11916908-11929481	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv557575	chr12:11916908-11929481	Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv832331	chr12:11925095-12114451	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:11908600-11931800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:11909600-11932400	Genic enhancers	Fetal Thymus	thymus
3	chr12:11915400-11938000	Weak transcription	NHEK	skin
4	chr12:11915600-11938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:11918000-11936000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:11919400-11935000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:11919600-11932000	Weak transcription	HSMM	muscle
8	chr12:11919600-11936200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:11919600-11936800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:11919800-11929400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:11919800-11931400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:11919800-11932400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:11920000-11929600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:11920000-11931800	Weak transcription	HSMMtube	muscle
15	chr12:11920000-11937800	Weak transcription	NHLF	lung
16	chr12:11921200-11930800	Weak transcription	Fetal Lung	lung
17	chr12:11921200-11931200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:11921800-11946600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:11922000-11948200	Weak transcription	Colonic Mucosa	Colon
20	chr12:11923400-11930800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:11923400-11930800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:11923400-11930800	Weak transcription	Esophagus	oesophagus
23	chr12:11923400-11930800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:11923600-11934600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:11923600-11952000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:11924200-11930800	Weak transcription	Spleen	Spleen
27	chr12:11924200-11931000	Weak transcription	Right Atrium	heart
28	chr12:11924600-11930400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:11924800-11930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr12:11924800-11930800	Weak transcription	Right Ventricle	heart
31	chr12:11925000-11930800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:11925400-11930800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:11925600-11930800	Weak transcription	Osteobl	bone
34	chr12:11925600-11932000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:11925600-11932000	Weak transcription	NH-A	brain
36	chr12:11925800-11929600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:11925800-11930800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:11925800-11938000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:11925800-11938000	Weak transcription	HMEC	breast
40	chr12:11926600-11936200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:11926800-11929200	Genic enhancers	Fetal Stomach	stomach
42	chr12:11927000-11930400	Weak transcription	Left Ventricle	heart
43	chr12:11927000-11930600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:11927000-11931000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:11927000-11936000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:11927200-11929200	Enhancers	Thymus	Thymus
47	chr12:11927200-11930400	Weak transcription	Psoas Muscle	Psoas
48	chr12:11927200-11930800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:11927200-11930800	Weak transcription	Liver	Liver
50	chr12:11927400-11929800	Strong transcription	Sigmoid Colon	Sigmoid Colon

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