Variant report

Variant	rs9645411
Chromosome Location	chr1:62279594-62279595
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	chr1:62207401..62209297-chr1:62277222..62279728,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271200	Chromatin interaction
ENSG00000132849	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10889256	0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs11207831	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207837	0.93[ASW][hapmap];0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs11207842	0.84[EUR][1000 genomes]
rs11207844	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11580167	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038135	0.87[TSI][hapmap]
rs12135784	0.83[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs12403946	0.81[EUR][1000 genomes]
rs12407806	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12755345	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3790576	0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3790577	0.91[TSI][hapmap]
rs4418641	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4915777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4915778	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4915779	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4915781	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4915782	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61770137	0.87[EUR][1000 genomes]
rs6661185	0.84[EUR][1000 genomes]
rs7516332	0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7519647	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7529082	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530529	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1099	chr1:62275317-62315943	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62220200-62290200	Weak transcription	Lung	lung
2	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:62222000-62293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:62224000-62290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:62225000-62284400	Weak transcription	Psoas Muscle	Psoas
6	chr1:62227800-62294600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
8	chr1:62233400-62288800	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:62235400-62288800	Weak transcription	A549	lung
10	chr1:62247600-62287400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:62247600-62297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:62250000-62302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:62251200-62288600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:62251200-62306400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:62253600-62297400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:62253800-62289000	Weak transcription	HepG2	liver
17	chr1:62254000-62286400	Weak transcription	Aorta	Aorta
18	chr1:62254000-62288600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:62254200-62288400	Weak transcription	Adipose Nuclei	Adipose
20	chr1:62255600-62302400	Weak transcription	Brain Anterior Caudate	brain
21	chr1:62257000-62291600	Weak transcription	Gastric	stomach
22	chr1:62263400-62280800	Weak transcription	Esophagus	oesophagus
23	chr1:62263400-62293200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:62263600-62288400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:62263800-62303800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
27	chr1:62264200-62290200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:62264600-62283800	Weak transcription	Primary T cells from cord blood	blood
29	chr1:62264600-62286400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:62264600-62286400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:62264600-62287800	Weak transcription	Left Ventricle	heart
32	chr1:62264600-62292800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:62264600-62296000	Weak transcription	Fetal Brain Female	brain
34	chr1:62264600-62297400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:62264600-62321600	Weak transcription	Pancreas	Pancrea
36	chr1:62264600-62335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:62265200-62293000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:62265400-62293200	Weak transcription	Fetal Stomach	stomach
39	chr1:62265600-62284000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:62265600-62288400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr1:62266000-62284400	Weak transcription	Fetal Kidney	kidney
42	chr1:62266600-62288200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:62270800-62290200	Weak transcription	Stomach Mucosa	stomach
44	chr1:62271800-62283800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:62271800-62286400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:62271800-62329800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:62272000-62283800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:62272000-62283800	Weak transcription	HMEC	breast
49	chr1:62272000-62287200	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:62272000-62290200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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