Variant report

Variant	rs28409017
Chromosome Location	chr15:72147659-72147660
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	chr15:72132772..72134478-chr15:72147156..72150104,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs11072334	1.00[AFR][1000 genomes]
rs12101366	1.00[AFR][1000 genomes]
rs12101856	0.81[AFR][1000 genomes]
rs12102227	1.00[AFR][1000 genomes]
rs13329116	1.00[AFR][1000 genomes]
rs13329270	1.00[AFR][1000 genomes]
rs28367264	1.00[AFR][1000 genomes]
rs28373432	1.00[AFR][1000 genomes]
rs28379334	0.81[AFR][1000 genomes]
rs28397143	1.00[AFR][1000 genomes]
rs28397237	1.00[AFR][1000 genomes]
rs28397783	1.00[AFR][1000 genomes]
rs28403882	0.81[AFR][1000 genomes]
rs28408067	1.00[AFR][1000 genomes]
rs28409864	0.84[AFR][1000 genomes]
rs28412105	1.00[AFR][1000 genomes]
rs28413902	1.00[AFR][1000 genomes]
rs28416103	0.91[AFR][1000 genomes]
rs28421817	0.91[AFR][1000 genomes]
rs28428645	1.00[AFR][1000 genomes]
rs28429589	1.00[AFR][1000 genomes]
rs28430988	1.00[AFR][1000 genomes]
rs28445807	1.00[AFR][1000 genomes]
rs28449356	1.00[AFR][1000 genomes]
rs28450424	1.00[AFR][1000 genomes]
rs28451732	1.00[AFR][1000 genomes]
rs28455090	1.00[AFR][1000 genomes]
rs28465335	1.00[AFR][1000 genomes]
rs28470660	1.00[AFR][1000 genomes]
rs28482979	1.00[AFR][1000 genomes]
rs28483934	1.00[AFR][1000 genomes]
rs28485920	1.00[AFR][1000 genomes]
rs28501562	1.00[AFR][1000 genomes]
rs28502516	0.91[AFR][1000 genomes]
rs28514321	1.00[AFR][1000 genomes]
rs28515972	0.81[AFR][1000 genomes]
rs28529658	0.81[AFR][1000 genomes]
rs28535954	1.00[AFR][1000 genomes]
rs28536592	1.00[AFR][1000 genomes]
rs28542557	1.00[AFR][1000 genomes]
rs28548453	1.00[AFR][1000 genomes]
rs28569017	1.00[AFR][1000 genomes]
rs28570214	1.00[AFR][1000 genomes]
rs28573725	0.82[AFR][1000 genomes]
rs28578220	1.00[AFR][1000 genomes]
rs28583168	1.00[AFR][1000 genomes]
rs28589979	1.00[AFR][1000 genomes]
rs28599944	1.00[AFR][1000 genomes]
rs28605814	0.81[AFR][1000 genomes]
rs28618096	1.00[AFR][1000 genomes]
rs28625307	1.00[AFR][1000 genomes]
rs28630701	1.00[AFR][1000 genomes]
rs28634283	1.00[AFR][1000 genomes]
rs28636054	1.00[AFR][1000 genomes]
rs28639590	1.00[AFR][1000 genomes]
rs28642081	0.81[AFR][1000 genomes]
rs28643497	1.00[AFR][1000 genomes]
rs28654176	1.00[AFR][1000 genomes]
rs28654861	0.82[AFR][1000 genomes]
rs28660217	0.84[AFR][1000 genomes]
rs28662800	1.00[AFR][1000 genomes]
rs28670261	1.00[AFR][1000 genomes]
rs28675378	1.00[AFR][1000 genomes]
rs28676909	1.00[AFR][1000 genomes]
rs28681225	1.00[AFR][1000 genomes]
rs28690018	1.00[AFR][1000 genomes]
rs28701136	1.00[AFR][1000 genomes]
rs28705696	1.00[AFR][1000 genomes]
rs28707565	0.81[AFR][1000 genomes]
rs28709937	1.00[AFR][1000 genomes]
rs28715777	0.81[AFR][1000 genomes]
rs28725466	1.00[AFR][1000 genomes]
rs28727443	1.00[AFR][1000 genomes]
rs28741048	1.00[AFR][1000 genomes]
rs28778881	1.00[AFR][1000 genomes]
rs28786091	1.00[AFR][1000 genomes]
rs28791192	0.91[AFR][1000 genomes]
rs28801155	1.00[AFR][1000 genomes]
rs28808678	1.00[AFR][1000 genomes]
rs28809863	1.00[AFR][1000 genomes]
rs28812537	1.00[AFR][1000 genomes]
rs28817677	1.00[AFR][1000 genomes]
rs28824293	1.00[AFR][1000 genomes]
rs28830268	1.00[AFR][1000 genomes]
rs28833566	1.00[AFR][1000 genomes]
rs28853032	1.00[AFR][1000 genomes]
rs28872877	0.81[AFR][1000 genomes]
rs28879707	1.00[AFR][1000 genomes]
rs9888653	1.00[AFR][1000 genomes]
rs9920204	1.00[AFR][1000 genomes]
rs9920223	1.00[AFR][1000 genomes]
rs9920476	1.00[AFR][1000 genomes]
rs9920987	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569906	chr15:72126034-72218036	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv516871	chr15:72126034-72325595	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1042740	chr15:72128799-72482239	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv542426	chr15:72128799-72482239	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv904336	chr15:72145937-72329906	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72114600-72190600	Weak transcription	Pancreas	Pancrea
2	chr15:72119200-72171800	Weak transcription	Psoas Muscle	Psoas
3	chr15:72122200-72189400	Weak transcription	Right Ventricle	heart
4	chr15:72122400-72195000	Weak transcription	NHEK	skin
5	chr15:72122600-72171800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:72122600-72185200	Weak transcription	Esophagus	oesophagus
7	chr15:72122600-72195800	Weak transcription	Gastric	stomach
8	chr15:72129200-72148000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:72131200-72148200	Strong transcription	Placenta	Placenta
10	chr15:72131800-72192800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr15:72134000-72149000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:72136200-72148400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr15:72136200-72148400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:72136200-72149000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:72136400-72148400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:72137000-72156400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:72138200-72172400	Weak transcription	HUVEC	blood vessel
18	chr15:72140200-72171800	Weak transcription	HMEC	breast
19	chr15:72141400-72174200	Weak transcription	Fetal Brain Male	brain
20	chr15:72142600-72150800	Weak transcription	HSMM	muscle
21	chr15:72142600-72151200	Weak transcription	HSMMtube	muscle
22	chr15:72142600-72151400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr15:72142600-72154000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:72142600-72154600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:72142600-72166400	Weak transcription	GM12878-XiMat	blood
26	chr15:72142600-72170200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:72142600-72171800	Weak transcription	NH-A	brain
28	chr15:72142600-72183400	Weak transcription	Brain Angular Gyrus	brain
29	chr15:72142600-72189600	Weak transcription	NHLF	lung
30	chr15:72142600-72199200	Weak transcription	Hela-S3	cervix
31	chr15:72142800-72151200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:72142800-72151200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:72142800-72170000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:72142800-72171800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:72142800-72172000	Weak transcription	Dnd41	blood
36	chr15:72142800-72176000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:72142800-72184800	Weak transcription	A549	lung
38	chr15:72142800-72190200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:72143000-72149000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:72143000-72163400	Weak transcription	Fetal Intestine Small	intestine
41	chr15:72143000-72172200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:72143000-72190600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:72143000-72190600	Weak transcription	Colonic Mucosa	Colon
44	chr15:72143200-72152000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:72143200-72152200	Weak transcription	Brain Substantia Nigra	brain
46	chr15:72143400-72151400	Weak transcription	Fetal Kidney	kidney
47	chr15:72143800-72152000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr15:72143800-72160200	Weak transcription	Aorta	Aorta
49	chr15:72143800-72172000	Weak transcription	Brain Germinal Matrix	brain
50	chr15:72144000-72166400	Weak transcription	Ovary	ovary

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