Variant report

Variant	rs13239000
Chromosome Location	chr7:116543714-116543715
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	chr7:116536819..116538924-chr7:116542364..116544678,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10487354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533755	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12537847	0.91[YRI][hapmap]
rs12665952	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669383	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12670056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12671827	0.99[EUR][1000 genomes]
rs12671828	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12672008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12673979	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12674017	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12706108	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706109	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12706110	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706112	0.95[EUR][1000 genomes]
rs12706115	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706120	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12706121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706122	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12706123	0.81[EUR][1000 genomes]
rs13222845	0.99[EUR][1000 genomes]
rs13224082	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13228847	0.94[EUR][1000 genomes]
rs2237718	0.91[YRI][hapmap]
rs2237720	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299441	0.92[EUR][1000 genomes]
rs2301649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3173936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3807999	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs4808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808129	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9791492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][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	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 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	chr7:116503800-116554400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:116506000-116554600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:116511400-116554600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:116512000-116545400	Weak transcription	NHLF	lung
5	chr7:116515400-116559200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:116516800-116551200	Weak transcription	Brain Angular Gyrus	brain
7	chr7:116517200-116554600	Weak transcription	Esophagus	oesophagus
8	chr7:116517600-116556600	Weak transcription	Psoas Muscle	Psoas
9	chr7:116520000-116551200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr7:116524600-116543800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:116525800-116551200	Weak transcription	Thymus	Thymus
12	chr7:116525800-116554600	Weak transcription	Aorta	Aorta
13	chr7:116525800-116558400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:116525800-116559400	Weak transcription	Colonic Mucosa	Colon
15	chr7:116526000-116543800	Weak transcription	Lung	lung
16	chr7:116526200-116550000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr7:116526200-116551200	Weak transcription	Small Intestine	intestine
18	chr7:116526600-116545400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:116526600-116553600	Weak transcription	Right Ventricle	heart
20	chr7:116526800-116546800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:116526800-116554600	Weak transcription	Gastric	stomach
22	chr7:116526800-116559400	Weak transcription	Stomach Mucosa	stomach
23	chr7:116527000-116543800	Weak transcription	Ovary	ovary
24	chr7:116527000-116546200	Weak transcription	Brain Anterior Caudate	brain
25	chr7:116527000-116560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:116527200-116549600	Weak transcription	Fetal Heart	heart
27	chr7:116530200-116550200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:116531400-116550600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr7:116531600-116548400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr7:116532000-116551200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr7:116532000-116559600	Strong transcription	HSMM	muscle
32	chr7:116534000-116543800	Weak transcription	HSMMtube	muscle
33	chr7:116534000-116546600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr7:116534200-116546400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:116534200-116546400	Weak transcription	Brain Hippocampus Middle	brain
36	chr7:116534400-116551800	Weak transcription	Fetal Stomach	stomach
37	chr7:116535600-116552000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:116537600-116551200	Weak transcription	Brain Germinal Matrix	brain
39	chr7:116537800-116545400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:116537800-116551400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:116538000-116559600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr7:116538200-116562400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:116538400-116551200	Weak transcription	NHEK	skin
44	chr7:116538600-116545400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:116538600-116545400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:116538600-116554200	Weak transcription	Spleen	Spleen
47	chr7:116538600-116559400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:116538800-116547400	Strong transcription	A549	lung
49	chr7:116539200-116548000	Strong transcription	NH-A	brain
50	chr7:116539400-116548600	Strong transcription	Liver	Liver

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