Variant report

Variant	rs60053512
Chromosome Location	chr17:60095315-60095316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr17:60095244-60095846	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr17:60094392-60095913	MCF-7	breast:	n/a	n/a
3	TCF7L2	chr17:60094501-60095781	MCF-7	breast:	n/a	n/a
4	POLR2A	chr17:60094880-60095463	MCF-7	breast:	n/a	n/a
5	ZNF217	chr17:60094455-60095884	MCF-7	breast:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:60094989..60096269-chr17:60188609..60189856,6	MCF-7	breast:
2	chr17:60094632..60096266-chr17:60187770..60189403,13	MCF-7	breast:
3	chr17:60094034..60095427-chr20:54158893..54160051,10	MCF-7	breast:
4	chr17:60094004..60095670-chr20:54158803..54160304,7	MCF-7	breast:
5	chr17:60095074..60095939-chr3:121314935..121315693,2	MCF-7	breast:
6	chr17:60093997..60095651-chr20:54158793..54160830,19	MCF-7	breast:
7	chr17:60080672..60083062-chr17:60094913..60097385,2	MCF-7	breast:
8	chr17:60094719..60096261-chr17:60187728..60188632,14	MCF-7	breast:
9	chr17:60093994..60095685-chr20:54158785..54160774,22	MCF-7	breast:
10	chr17:60095214..60096265-chr17:60187776..60188537,6	MCF-7	breast:
11	chr17:60094562..60096237-chr17:60187742..60189867,14	MCF-7	breast:
12	chr17:60094652..60097882-chr17:60102443..60104889,3	MCF-7	breast:
13	chr17:60094995..60095643-chr2:38829069..38830044,2	MCF-7	breast:
14	chr17:60094021..60095602-chr20:54158807..54160279,10	MCF-7	breast:
15	chr17:60094752..60095718-chr20:54160361..54161333,2	MCF-7	breast:
16	chr17:60093422..60097278-chr17:60186745..60191637,29	MCF-7	breast:
17	chr17:60094884..60097281-chr17:60186748..60190045,19	MCF-7	breast:
18	chr17:60090504..60092399-chr17:60094678..60097577,2	MCF-7	breast:
19	chr17:60094978..60095699-chr17:60190204..60190813,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000221302	TF binding region
ENSG00000143889	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];1.00[ASN][1000 genomes]
rs11079459	0.84[AFR][1000 genomes]
rs12450223	0.86[ASN][1000 genomes]
rs12450560	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12452094	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12600620	0.89[EUR][1000 genomes];0.88[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];1.00[ASN][1000 genomes]
rs16945756	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945759	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16945801	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278812	0.86[ASN][1000 genomes]
rs28654524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809753	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826419	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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];0.82[ASN][1000 genomes]
rs4968463	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968464	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4968467	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968468	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968470	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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];0.94[ASN][1000 genomes]
rs57746689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.98[ASN][1000 genomes]
rs58335059	1.00[ASN][1000 genomes]
rs59080342	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61469058	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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];0.98[ASN][1000 genomes]
rs7221089	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843781	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs73334621	0.83[EUR][1000 genomes]
rs73336436	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8065778	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066964	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8074890	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9630736	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	chr17:60021200-60097000	Strong transcription	Dnd41	blood
2	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
4	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
5	chr17:60048800-60097600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:60050200-60100800	Weak transcription	Small Intestine	intestine
7	chr17:60060400-60096200	Weak transcription	Fetal Brain Male	brain
8	chr17:60060400-60098800	Weak transcription	Gastric	stomach
9	chr17:60060400-60099800	Weak transcription	Aorta	Aorta
10	chr17:60061600-60099600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr17:60062400-60106800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:60069200-60107600	Weak transcription	Spleen	Spleen
13	chr17:60069600-60099000	Weak transcription	Colonic Mucosa	Colon
14	chr17:60072400-60100600	Weak transcription	Right Ventricle	heart
15	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
16	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
18	chr17:60077800-60099800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:60080200-60099000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:60081400-60096400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:60081800-60111600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr17:60082000-60096200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:60083400-60098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:60083600-60096400	Weak transcription	Brain Germinal Matrix	brain
25	chr17:60084600-60099000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr17:60086000-60096600	Strong transcription	HepG2	liver
27	chr17:60086200-60097600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr17:60086400-60097600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr17:60087000-60097400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr17:60087000-60102200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr17:60088400-60098800	Weak transcription	Colon Smooth Muscle	Colon
32	chr17:60088400-60099000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr17:60088400-60099200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr17:60088400-60107600	Weak transcription	Pancreas	Pancrea
35	chr17:60088600-60095800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr17:60088600-60096200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:60088600-60097000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr17:60088600-60098800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr17:60088600-60099000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr17:60088600-60099000	Weak transcription	Brain Substantia Nigra	brain
41	chr17:60088600-60099000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:60088600-60099200	Weak transcription	Lung	lung
43	chr17:60088600-60100000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr17:60088600-60100200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr17:60088600-60100200	Weak transcription	Ovary	ovary
46	chr17:60088600-60100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:60088600-60100600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr17:60088600-60100800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr17:60088600-60105200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:60088600-60105400	Weak transcription	Esophagus	oesophagus

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