Variant report

Variant	rs4447799
Chromosome Location	chr3:105584684-105584685
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	chr3:105579577..105582453-chr3:105582537..105585477,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10804442	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10933833	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711088	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11924742	0.92[CEU][hapmap]
rs12636287	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13060223	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13085563	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13100446	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1443102	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1470283	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867192	0.86[CEU][hapmap]
rs1867195	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1910499	0.85[CEU][hapmap]
rs1992522	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2055557	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2089091	0.85[CEU][hapmap]
rs2099892	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197209	0.86[CEU][hapmap]
rs2399056	0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28427229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28533328	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3996189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243427	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894950	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894953	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894954	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4894957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894960	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894962	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6437621	0.86[CEU][hapmap]
rs6437624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767627	0.85[CEU][hapmap]
rs6788366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795961	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6804152	0.81[EUR][1000 genomes]
rs6807382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71627856	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7432372	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7629357	0.86[CEU][hapmap]
rs7637327	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645021	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647955	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs769315	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9657904	0.85[CEU][hapmap]
rs971110	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9841500	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846534	0.86[CEU][hapmap]
rs9869648	0.86[CEU][hapmap]
rs9874600	0.85[CEU][hapmap]

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:124 , 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	chr3:105564800-105585000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:105565600-105584800	Weak transcription	NHEK	skin
9	chr3:105566200-105584800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:105566200-105585000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:105568000-105586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:105568000-105586200	Weak transcription	Pancreas	Pancrea
13	chr3:105568800-105586200	Weak transcription	Colonic Mucosa	Colon
14	chr3:105569800-105586200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:105572000-105586200	Weak transcription	Lung	lung
16	chr3:105572200-105585000	Weak transcription	Thymus	Thymus
17	chr3:105572200-105585400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:105572600-105585200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:105572600-105585800	Weak transcription	Fetal Thymus	thymus
20	chr3:105572800-105585800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:105573200-105585000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:105579400-105584800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:105579400-105585000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:105579800-105585600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:105579800-105585800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:105581400-105585600	Weak transcription	Aorta	Aorta
27	chr3:105581600-105585200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
28	chr3:105581800-105586200	Weak transcription	Gastric	stomach
29	chr3:105581800-105588800	Active TSS	Right Ventricle	heart
30	chr3:105582000-105585400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
31	chr3:105582200-105588200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:105582200-105589000	Active TSS	Right Atrium	heart
33	chr3:105582400-105584800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:105582400-105584800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:105582600-105585000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:105582600-105585400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:105582800-105585000	Enhancers	HepG2	liver
38	chr3:105582800-105585200	Genic enhancers	Dnd41	blood
39	chr3:105582800-105585600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:105582800-105585800	Transcr. at gene 5' and 3'	Osteobl	bone
41	chr3:105582800-105586200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:105583000-105585200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:105583000-105585800	Enhancers	Fetal Intestine Small	intestine
44	chr3:105583200-105584800	Enhancers	Brain Hippocampus Middle	brain
45	chr3:105583200-105586200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:105583200-105586200	Enhancers	Hela-S3	cervix
47	chr3:105583200-105586800	Weak transcription	Spleen	Spleen
48	chr3:105583400-105584800	Weak transcription	HMEC	breast
49	chr3:105583400-105585600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr3:105583400-105586000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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