Variant report

Variant	rs28417081
Chromosome Location	chr15:52775561-52775562
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52774259..52776671-chr15:52790195..52792065,2	MCF-7	breast:
2	chr15:52775070..52777888-chr15:52820871..52822715,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13329510	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1693516	1.00[EUR][1000 genomes]
rs1693517	1.00[EUR][1000 genomes]
rs1693519	1.00[EUR][1000 genomes]
rs1724599	1.00[EUR][1000 genomes]
rs1724600	1.00[EUR][1000 genomes]
rs1724602	1.00[EUR][1000 genomes]
rs2222656	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28401713	1.00[ASN][1000 genomes]
rs28417825	1.00[EUR][1000 genomes]
rs28421476	1.00[AMR][1000 genomes]
rs28483042	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28485251	1.00[AMR][1000 genomes]
rs28485735	0.87[ASN][1000 genomes]
rs28499517	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28510975	1.00[ASN][1000 genomes]
rs28545705	1.00[ASN][1000 genomes]
rs28556791	1.00[EUR][1000 genomes]
rs28570350	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28578651	1.00[ASN][1000 genomes]
rs28581262	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613360	1.00[AMR][1000 genomes]
rs28642806	1.00[ASN][1000 genomes]
rs28663524	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28665952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673564	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28682547	1.00[EUR][1000 genomes]
rs28687913	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28699673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729511	1.00[EUR][1000 genomes]
rs28761013	0.87[ASN][1000 genomes]
rs28786736	0.87[ASN][1000 genomes]
rs28795685	0.87[ASN][1000 genomes]
rs28814017	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28814321	0.87[ASN][1000 genomes]
rs28840839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28876722	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3764226	0.88[ASN][1000 genomes]
rs7168981	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73412972	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73412975	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342673	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920195	0.86[AFR][1000 genomes];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	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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52759200-52778200	Weak transcription	Right Atrium	heart
2	chr15:52770000-52776600	Enhancers	Primary T cells fromperipheralblood	blood
3	chr15:52770000-52777000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:52770800-52776400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:52771000-52777000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr15:52771000-52778000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:52771400-52776200	Enhancers	Fetal Thymus	thymus
8	chr15:52771400-52776400	Enhancers	Primary hematopoietic stem cells	blood
9	chr15:52771400-52776400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:52771800-52776200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr15:52772000-52775600	Enhancers	Duodenum Mucosa	Duodenum
12	chr15:52772000-52775800	Enhancers	HUVEC	blood vessel
13	chr15:52772000-52776400	Enhancers	Primary B cells from peripheral blood	blood
14	chr15:52772000-52776600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:52772000-52776800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:52772000-52776800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr15:52772000-52777000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr15:52772000-52777000	Enhancers	NHDF-Ad	bronchial
19	chr15:52772200-52776400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:52772200-52776600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr15:52772200-52781600	Weak transcription	Colonic Mucosa	Colon
22	chr15:52772600-52777200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr15:52772600-52777200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:52772800-52776400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:52772800-52776400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr15:52772800-52776800	Enhancers	HMEC	breast
27	chr15:52773000-52776000	Enhancers	Brain Hippocampus Middle	brain
28	chr15:52773000-52776200	Enhancers	NHLF	lung
29	chr15:52773000-52776600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:52773000-52776600	Enhancers	Brain Anterior Caudate	brain
31	chr15:52773000-52776800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:52773000-52776800	Enhancers	Osteobl	bone
33	chr15:52773000-52777000	Enhancers	NHEK	skin
34	chr15:52773200-52776800	Enhancers	NH-A	brain
35	chr15:52773600-52776800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:52774000-52775600	Enhancers	Psoas Muscle	Psoas
37	chr15:52774000-52776600	Enhancers	HSMMtube	muscle
38	chr15:52774200-52776000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr15:52774200-52776000	Enhancers	Primary T cells from cord blood	blood
40	chr15:52774400-52777000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:52774600-52775600	Weak transcription	Adipose Nuclei	Adipose
42	chr15:52774600-52776000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:52774600-52776400	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr15:52774600-52776600	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr15:52774600-52776600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:52774600-52776800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:52774600-52777000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:52774600-52777000	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr15:52774600-52777200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:52774600-52778200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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