Variant report

Variant	rs6504066
Chromosome Location	chr17:59802506-59802507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59800856..59804163-chr17:59876065..59879949,4	MCF-7	breast:
2	chr17:59489613..59491206-chr17:59800419..59803266,2	MCF-7	breast:
3	chr17:59802211..59804083-chr20:55691299..55693617,2	MCF-7	breast:
4	chr17:59800860..59802711-chr9:132596454..132599120,2	MCF-7	breast:
5	chr17:59801364..59804296-chr6:151936458..151938783,2	MCF-7	breast:
6	chr17:59801899..59802799-chr17:59877268..59878115,2	MCF-7	breast:
7	chr17:59800566..59802805-chr3:64485912..64488296,2	MCF-7	breast:
8	chr17:59802319..59804545-chr20:50350734..50353080,2	MCF-7	breast:
9	chr17:59799068..59802812-chr17:59939029..59942892,4	MCF-7	breast:
10	chr17:59800446..59802720-chr17:59893670..59895500,2	MCF-7	breast:
11	chr17:59801109..59803625-chr8:101320526..101322625,2	MCF-7	breast:
12	chr17:59799787..59802608-chr17:59908200..59910482,3	MCF-7	breast:
13	chr17:59798896..59803310-chr17:59938470..59941648,4	MCF-7	breast:
14	chr1:156142245..156144715-chr17:59800161..59802589,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215444	Chromatin interaction
ENSG00000034677	Chromatin interaction
ENSG00000136819	Chromatin interaction
ENSG00000207422	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000136878	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1015771	0.95[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs10221278	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[TSI][hapmap]
rs10438771	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs10468558	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs10515206	1.00[CEU][hapmap]
rs10515207	0.94[CEU][hapmap];0.82[CHB][hapmap]
rs10515211	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs10853038	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs11079445	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs11650471	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs11871753	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs12451862	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12453801	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs12453935	0.80[MEX][hapmap]
rs12453966	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs12603617	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs12949659	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs1468577	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs1541346	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs1978244	0.90[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs1990338	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs2040608	1.00[CEU][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs2191249	0.95[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs2378905	0.90[CEU][hapmap]
rs2890012	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs2890013	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2890021	0.95[CEU][hapmap]
rs4968444	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs4968447	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs4968582	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs6504068	0.95[CEU][hapmap]
rs6504071	0.94[CEU][hapmap]
rs6504072	0.90[CEU][hapmap]
rs717961	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs717962	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7207074	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7207881	0.95[CEU][hapmap]
rs7208704	0.94[CEU][hapmap]
rs7212172	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs7212423	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap]
rs7213329	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs7213587	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7214884	0.87[CEU][hapmap]
rs7215784	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs7216756	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs7217206	0.94[CEU][hapmap]
rs7220688	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs7220719	0.83[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs7222799	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs8075370	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs8078977	0.84[CEU][hapmap]
rs8182296	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs9303449	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs9895987	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs9897121	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs9897928	0.95[CEU][hapmap]
rs9902995	0.95[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs9904292	0.90[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs9906313	0.95[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs9907299	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv908674	chr17:59800827-59899790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59766000-59819000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr17:59778200-59805800	Weak transcription	Thymus	Thymus
3	chr17:59781600-59835400	Weak transcription	Hela-S3	cervix
4	chr17:59784400-59815200	Weak transcription	HMEC	breast
5	chr17:59786600-59815400	Weak transcription	Fetal Thymus	thymus
6	chr17:59792000-59815200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:59793200-59803400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:59793200-59819400	Weak transcription	NH-A	brain
9	chr17:59793600-59821200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:59794200-59815200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:59794200-59819600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr17:59794400-59815200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:59794400-59816200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr17:59794400-59848200	Weak transcription	HUVEC	blood vessel
15	chr17:59794600-59807200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:59794800-59806000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:59794800-59815200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:59796200-59805600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr17:59796200-59805800	Weak transcription	A549	lung
20	chr17:59796200-59814400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:59797400-59817600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr17:59797600-59813000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr17:59798200-59803400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:59798400-59803400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:59798400-59815000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:59798800-59816400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr17:59800800-59803000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:59800800-59814400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr17:59801000-59803000	Weak transcription	Dnd41	blood
30	chr17:59801000-59815400	Weak transcription	HepG2	liver
31	chr17:59801200-59817400	Weak transcription	Small Intestine	intestine
32	chr17:59801600-59805800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:59801600-59815000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:59801600-59816200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:59802000-59808600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr17:59802200-59802800	Weak transcription	Fetal Lung	lung

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