Variant report

Variant	rs6701709
Chromosome Location	chr1:220954103-220954104
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	chr1:220953456..220955910-chr1:220956929..220958618,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11118601	0.96[AMR][1000 genomes]
rs1690716	0.82[ASN][1000 genomes]
rs3820354	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs3820356	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57298117	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58327003	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58438675	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59234976	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6541159	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682431	0.93[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6683301	0.90[ASN][1000 genomes]
rs72470566	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72470578	0.94[AMR][1000 genomes]
rs72470579	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72470580	0.94[AMR][1000 genomes]
rs72470582	0.94[AMR][1000 genomes]
rs7526347	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7537305	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868494	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9970238	0.90[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523389	chr1:220926844-220956012	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
4	chr1:220930000-220959600	Weak transcription	Psoas Muscle	Psoas
5	chr1:220930400-220959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:220931200-220959000	Weak transcription	Brain Substantia Nigra	brain
7	chr1:220936200-220959600	Weak transcription	A549	lung
8	chr1:220936600-220958200	Weak transcription	Esophagus	oesophagus
9	chr1:220939000-220960400	Weak transcription	Small Intestine	intestine
10	chr1:220943000-220958400	Weak transcription	HepG2	liver
11	chr1:220943000-220959000	Strong transcription	Fetal Intestine Large	intestine
12	chr1:220944200-220956000	Weak transcription	Pancreas	Pancrea
13	chr1:220944200-220959200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:220944200-220959400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:220944200-220959400	Weak transcription	Fetal Kidney	kidney
16	chr1:220944200-220959600	Weak transcription	NHLF	lung
17	chr1:220944200-220959800	Weak transcription	Gastric	stomach
18	chr1:220944400-220954600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:220944400-220956000	Weak transcription	Aorta	Aorta
20	chr1:220944400-220956800	Weak transcription	Spleen	Spleen
21	chr1:220944400-220958800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:220944400-220959000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:220944400-220959200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:220944400-220959400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:220944400-220959400	Weak transcription	Colonic Mucosa	Colon
26	chr1:220944400-220959400	Weak transcription	Right Ventricle	heart
27	chr1:220945800-220959200	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:220946000-220956800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:220946400-220956200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:220946600-220958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:220946800-220958800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:220949800-220954200	Strong transcription	Fetal Intestine Small	intestine
33	chr1:220950200-220957800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:220950200-220959200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:220950400-220958000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:220950400-220959400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:220950600-220954400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:220950600-220958000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:220950600-220958800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:220950600-220959000	Weak transcription	Fetal Heart	heart
41	chr1:220950600-220959400	Weak transcription	Right Atrium	heart
42	chr1:220951000-220954600	Strong transcription	Liver	Liver
43	chr1:220951200-220956800	Weak transcription	Hela-S3	cervix
44	chr1:220951600-220954200	Strong transcription	Left Ventricle	heart
45	chr1:220952000-220957800	Strong transcription	Fetal Lung	lung
46	chr1:220952400-220958800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:220953200-220957400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:220953200-220959600	Weak transcription	Lung	lung
49	chr1:220953400-220957800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:220953600-220955200	Weak transcription	Fetal Muscle Leg	muscle

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