Variant report

Variant	rs7519647
Chromosome Location	chr1:62262241-62262242
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	chr1:62206940..62209583-chr1:62260283..62262996,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271200	Chromatin interaction
ENSG00000132849	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10889256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11207831	0.83[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11207837	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs11207842	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11207844	0.82[EUR][1000 genomes]
rs11580167	0.84[EUR][1000 genomes]
rs12038135	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs12045055	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12135784	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12403946	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12407806	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3790576	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3790577	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4418641	0.81[EUR][1000 genomes]
rs4915776	0.93[EUR][1000 genomes]
rs4915777	0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4915778	0.85[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4915779	0.85[EUR][1000 genomes]
rs4915781	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4915782	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61770137	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6661185	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7516332	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529082	0.87[EUR][1000 genomes]
rs7530529	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9645411	0.91[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62213600-62263200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:62220200-62290200	Weak transcription	Lung	lung
3	chr1:62220200-62310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:62221800-62263000	Weak transcription	Colonic Mucosa	Colon
5	chr1:62222000-62293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:62224000-62263000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:62224000-62267600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:62224000-62290800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:62224600-62263000	Weak transcription	Left Ventricle	heart
10	chr1:62225000-62284400	Weak transcription	Psoas Muscle	Psoas
11	chr1:62227800-62294600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
13	chr1:62231800-62273400	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:62232200-62262800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:62232800-62267200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:62233000-62263000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:62233200-62263800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:62233400-62264200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:62233400-62288800	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:62235400-62263200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:62235400-62288800	Weak transcription	A549	lung
22	chr1:62237600-62263000	Weak transcription	Fetal Brain Female	brain
23	chr1:62240200-62264600	Weak transcription	Right Ventricle	heart
24	chr1:62240800-62264800	Weak transcription	Hela-S3	cervix
25	chr1:62242200-62274400	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:62243000-62270600	Weak transcription	Spleen	Spleen
27	chr1:62247400-62263000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:62247600-62287400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:62247600-62297400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:62249800-62263000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:62250000-62263400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:62250000-62302800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:62251200-62268400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:62251200-62288600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:62251200-62306400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:62251400-62263000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:62251800-62272600	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:62252000-62275800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:62253000-62266600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:62253000-62274400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:62253600-62297400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:62253800-62262800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:62253800-62265400	Weak transcription	Fetal Kidney	kidney
44	chr1:62253800-62271200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:62253800-62289000	Weak transcription	HepG2	liver
46	chr1:62254000-62262400	Weak transcription	Pancreas	Pancrea
47	chr1:62254000-62262600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:62254000-62262800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:62254000-62263000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:62254000-62263000	Weak transcription	Ovary	ovary

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