Variant report

Variant	rs12902173
Chromosome Location	chr15:56259095-56259096
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56250089..56252612-chr15:56259045..56261387,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10518823	0.91[EUR][1000 genomes]
rs12439899	0.83[EUR][1000 genomes]
rs12898478	0.91[EUR][1000 genomes]
rs12901802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12904236	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12908286	0.81[EUR][1000 genomes]
rs12911101	0.81[EUR][1000 genomes]
rs17819270	0.93[EUR][1000 genomes]
rs1912397	0.91[EUR][1000 genomes]
rs1912403	0.93[EUR][1000 genomes]
rs34162982	1.00[EUR][1000 genomes]
rs34223710	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34333169	0.81[EUR][1000 genomes]
rs34652186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34718758	0.82[EUR][1000 genomes]
rs34727807	0.91[EUR][1000 genomes]
rs34995202	0.91[EUR][1000 genomes]
rs35086304	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35142499	0.96[EUR][1000 genomes]
rs35313340	0.81[EUR][1000 genomes]
rs35485562	0.83[EUR][1000 genomes]
rs4296197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66473405	0.83[EUR][1000 genomes]
rs66857236	0.91[EUR][1000 genomes]
rs67046147	0.93[EUR][1000 genomes]
rs67825863	0.91[EUR][1000 genomes]
rs71476753	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476755	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476760	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71476766	0.83[EUR][1000 genomes]
rs7172454	0.93[EUR][1000 genomes]
rs7182037	0.83[EUR][1000 genomes]
rs8038204	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039617	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042074	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8043427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs906811	1.00[AMR][1000 genomes];1.00[EUR][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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904245	chr15:56229760-56324451	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv457159	chr15:56255774-56321854	Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv569543	chr15:56255774-56321854	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56229400-56259400	Weak transcription	Small Intestine	intestine
2	chr15:56229600-56282600	Weak transcription	NHLF	lung
3	chr15:56231400-56284200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:56231600-56260000	Weak transcription	Left Ventricle	heart
5	chr15:56236000-56261200	Weak transcription	Esophagus	oesophagus
6	chr15:56236200-56276000	Weak transcription	HUVEC	blood vessel
7	chr15:56236800-56282800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:56241000-56261400	Weak transcription	Pancreas	Pancrea
9	chr15:56243200-56276200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:56248200-56285200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:56250000-56266600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:56251600-56281600	Weak transcription	Osteobl	bone
13	chr15:56252200-56261800	Weak transcription	Spleen	Spleen
14	chr15:56252400-56261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:56253200-56261200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:56253200-56261400	Weak transcription	HSMMtube	muscle
17	chr15:56253400-56261200	Weak transcription	Gastric	stomach
18	chr15:56253400-56261600	Weak transcription	Placenta	Placenta
19	chr15:56253400-56261800	Weak transcription	HMEC	breast
20	chr15:56253600-56282400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:56254000-56259600	Weak transcription	NHDF-Ad	bronchial
22	chr15:56254600-56262200	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:56255600-56261800	Weak transcription	Fetal Intestine Small	intestine
24	chr15:56257200-56261200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:56257600-56261000	Weak transcription	Hela-S3	cervix
26	chr15:56257600-56281600	Weak transcription	Fetal Intestine Large	intestine
27	chr15:56257600-56283600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:56257600-56283800	Weak transcription	Primary T cells from cord blood	blood
29	chr15:56257800-56259800	Weak transcription	NH-A	brain
30	chr15:56257800-56260400	Weak transcription	HSMM	muscle
31	chr15:56257800-56261000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:56257800-56261200	Weak transcription	Lung	lung
33	chr15:56257800-56261400	Weak transcription	Fetal Stomach	stomach
34	chr15:56257800-56270200	Weak transcription	Aorta	Aorta
35	chr15:56257800-56273800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:56258000-56260000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:56258000-56262000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:56258200-56261400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:56258400-56260000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:56258400-56261200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:56258400-56261400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr15:56258400-56261400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:56258400-56261400	Weak transcription	NHEK	skin
44	chr15:56258400-56262400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:56258400-56262600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:56258400-56262600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:56258400-56263800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:56258400-56265000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr15:56258600-56260800	Weak transcription	A549	lung

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