Variant report

Variant	rs12487841
Chromosome Location	chr3:105585956-105585957
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	chr3:105584001..105586223-chr3:105590379..105592467,2	MCF-7	breast:
2	chr3:105525619..105527234-chr3:105585628..105587643,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12485832	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486371	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496588	0.85[AMR][1000 genomes]
rs2089092	0.84[AMR][1000 genomes]
rs2455887	0.86[ASN][1000 genomes]
rs3772512	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344829	0.87[AMR][1000 genomes]
rs58882222	0.86[ASN][1000 genomes]
rs6437623	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778745	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791765	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793018	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796362	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997629	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997684	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639888	0.85[AMR][1000 genomes]
rs7650147	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820060	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841798	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876110	0.87[AMR][1000 genomes]
rs9880744	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1008564	chr3:105554580-105643435	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1008876	chr3:105554580-105645373	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv877312	chr3:105560638-105916506	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105546600-105586200	Weak transcription	Esophagus	oesophagus
2	chr3:105557800-105586200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:105558600-105586600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:105561600-105586200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:105562000-105586000	Weak transcription	K562	blood
6	chr3:105563000-105586800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
9	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
10	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:105572000-105586200	Weak transcription	Lung	lung
12	chr3:105581800-105586200	Weak transcription	Gastric	stomach
13	chr3:105581800-105588800	Active TSS	Right Ventricle	heart
14	chr3:105582200-105588200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:105582200-105589000	Active TSS	Right Atrium	heart
16	chr3:105582800-105586200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:105583200-105586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:105583200-105586200	Enhancers	Hela-S3	cervix
19	chr3:105583200-105586800	Weak transcription	Spleen	Spleen
20	chr3:105583400-105586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:105583600-105589000	Active TSS	Left Ventricle	heart
22	chr3:105584000-105586200	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
23	chr3:105584200-105586600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:105584200-105589200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:105584400-105586200	Enhancers	Brain Angular Gyrus	brain
26	chr3:105584400-105588600	Active TSS	HSMM	muscle
27	chr3:105584600-105586000	Flanking Active TSS	Fetal Heart	heart
28	chr3:105584600-105588600	Active TSS	Stomach Smooth Muscle	stomach
29	chr3:105584600-105589200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:105584800-105586000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr3:105584800-105588600	Active TSS	NHDF-Ad	bronchial
32	chr3:105585000-105586600	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr3:105585000-105586800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:105585000-105587600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:105585000-105588400	Active TSS	Primary T cells fromperipheralblood	blood
36	chr3:105585000-105588400	Active TSS	HMEC	breast
37	chr3:105585000-105588600	Active TSS	Fetal Stomach	stomach
38	chr3:105585200-105586200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr3:105585200-105586800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr3:105585200-105587200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:105585200-105587400	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr3:105585200-105588400	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr3:105585200-105588400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:105585200-105588400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr3:105585200-105588400	Active TSS	Placenta	Placenta
46	chr3:105585200-105588400	Active TSS	NH-A	brain
47	chr3:105585200-105588600	Active TSS	Muscle Satellite Cultured Cells	--
48	chr3:105585200-105588600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:105585200-105588600	Active TSS	Fetal Muscle Leg	muscle
50	chr3:105585200-105588600	Active TSS	HSMMtube	muscle

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