Variant report

Variant	rs28654524
Chromosome Location	chr17:60097657-60097658
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60003692..60006338-chr17:60096728..60098449,3	MCF-7	breast:
2	chr17:60094652..60097882-chr17:60102443..60104889,3	MCF-7	breast:
3	chr17:60097595..60100490-chr17:60100782..60103714,3	K562	blood:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10512492	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11079459	0.84[AFR][1000 genomes]
rs12450223	0.81[ASN][1000 genomes]
rs12450560	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12452094	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12600620	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12604037	0.89[EUR][1000 genomes]
rs16945753	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16945756	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16945759	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16945801	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278812	0.81[ASN][1000 genomes]
rs3809753	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3826419	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4410139	0.85[EUR][1000 genomes]
rs4968460	0.84[AFR][1000 genomes]
rs4968461	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4968462	0.84[AFR][1000 genomes]
rs4968463	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4968464	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4968467	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968468	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4968470	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56794817	0.81[AMR][1000 genomes]
rs57137451	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57746689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57918684	0.83[EUR][1000 genomes]
rs58241345	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58335059	0.95[ASN][1000 genomes]
rs59080342	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60053512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61469058	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61658218	0.84[EUR][1000 genomes]
rs7218724	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7221089	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72843781	0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73334621	0.83[EUR][1000 genomes]
rs73336436	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8065778	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8066964	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8074890	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9630736	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
3	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
4	chr17:60050200-60100800	Weak transcription	Small Intestine	intestine
5	chr17:60060400-60098800	Weak transcription	Gastric	stomach
6	chr17:60060400-60099800	Weak transcription	Aorta	Aorta
7	chr17:60061600-60099600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr17:60062400-60106800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr17:60069200-60107600	Weak transcription	Spleen	Spleen
10	chr17:60069600-60099000	Weak transcription	Colonic Mucosa	Colon
11	chr17:60072400-60100600	Weak transcription	Right Ventricle	heart
12	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
13	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
15	chr17:60077800-60099800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr17:60080200-60099000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:60081800-60111600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr17:60083400-60098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:60084600-60099000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:60087000-60102200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:60088400-60098800	Weak transcription	Colon Smooth Muscle	Colon
22	chr17:60088400-60099000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr17:60088400-60099200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr17:60088400-60107600	Weak transcription	Pancreas	Pancrea
25	chr17:60088600-60098800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:60088600-60099000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr17:60088600-60099000	Weak transcription	Brain Substantia Nigra	brain
28	chr17:60088600-60099000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr17:60088600-60099200	Weak transcription	Lung	lung
30	chr17:60088600-60100000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr17:60088600-60100200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr17:60088600-60100200	Weak transcription	Ovary	ovary
33	chr17:60088600-60100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr17:60088600-60100600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:60088600-60100800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr17:60088600-60105200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr17:60088600-60105400	Weak transcription	Esophagus	oesophagus
38	chr17:60088600-60106800	Weak transcription	Fetal Heart	heart
39	chr17:60088800-60099000	Weak transcription	Primary B cells from cord blood	blood
40	chr17:60088800-60099000	Weak transcription	HSMMtube	muscle
41	chr17:60088800-60099800	Weak transcription	Brain Anterior Caudate	brain
42	chr17:60089200-60099000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr17:60089200-60099600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr17:60089200-60100000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:60089200-60100600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:60089400-60099000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:60089400-60099200	Weak transcription	Left Ventricle	heart
48	chr17:60089600-60098800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:60090000-60099200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr17:60090600-60098800	Weak transcription	Brain Hippocampus Middle	brain

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