Variant report

Variant	rs2646030
Chromosome Location	chr15:52788750-52788751
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	chr15:52782555..52786559-chr15:52788524..52791233,4	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10851519	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12442200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1612233	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1693488	0.83[AMR][1000 genomes]
rs1693490	0.83[AMR][1000 genomes]
rs1693491	0.83[AMR][1000 genomes]
rs1693498	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1693503	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1693504	0.82[AFR][1000 genomes]
rs1724582	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1724619	0.82[AFR][1000 genomes]
rs2414157	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2453987	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2462852	0.83[AMR][1000 genomes]
rs2693464	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2693471	0.83[AMR][1000 genomes]
rs7176554	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52774600-52802600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:52776400-52789000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:52776400-52796200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:52776800-52788800	Weak transcription	Osteobl	bone
5	chr15:52778600-52788800	Weak transcription	HSMMtube	muscle
6	chr15:52778600-52812400	Weak transcription	Right Ventricle	heart
7	chr15:52779200-52791600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:52780200-52791800	Weak transcription	Brain Angular Gyrus	brain
9	chr15:52781400-52791000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:52781800-52795200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:52782400-52795600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:52782600-52796200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:52784000-52788800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:52784000-52788800	Weak transcription	NHLF	lung
15	chr15:52784400-52796400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:52784600-52789600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:52784600-52792200	Enhancers	HUVEC	blood vessel
18	chr15:52784800-52789000	Weak transcription	Brain Anterior Caudate	brain
19	chr15:52784800-52794800	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:52784800-52798800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:52785000-52791000	Weak transcription	Brain Substantia Nigra	brain
22	chr15:52785000-52801200	Weak transcription	Right Atrium	heart
23	chr15:52786400-52791200	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:52786400-52812400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:52786600-52788800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:52786600-52788800	Weak transcription	NH-A	brain
27	chr15:52786600-52796400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr15:52787000-52791200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:52787400-52789000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr15:52787400-52789000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:52787400-52791200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:52787800-52789400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:52787800-52789600	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr15:52788200-52788800	Enhancers	NHEK	skin
35	chr15:52788200-52789200	Enhancers	Primary B cells from peripheral blood	blood
36	chr15:52788200-52789600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr15:52788200-52789600	Enhancers	HMEC	breast
38	chr15:52788400-52789200	Enhancers	Primary B cells from cord blood	blood
39	chr15:52788400-52789200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:52788400-52789200	Enhancers	GM12878-XiMat	blood
41	chr15:52788400-52789200	Enhancers	NHDF-Ad	bronchial
42	chr15:52788400-52789400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr15:52788400-52789400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:52788400-52789400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:52788400-52789400	Enhancers	Esophagus	oesophagus
46	chr15:52788400-52789600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:52788400-52789600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr15:52788400-52789600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:52788400-52789600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:52788400-52789600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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