Variant report

Variant	rs9909664
Chromosome Location	chr17:59824831-59824832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:81478704..81480566-chr17:59823616..59825602,2	MCF-7	breast:
2	chr17:59757651..59759425-chr17:59822569..59825415,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153815	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11079449	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs11079450	1.00[AMR][1000 genomes]
rs16945451	1.00[AMR][1000 genomes]
rs16945455	1.00[AMR][1000 genomes]
rs16945466	1.00[AMR][1000 genomes]
rs16945472	1.00[AMR][1000 genomes]
rs16945489	1.00[AMR][1000 genomes]
rs16945495	0.86[ASW][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs16945522	1.00[AMR][1000 genomes]
rs2378882	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28409395	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28637035	1.00[AMR][1000 genomes]
rs28839618	1.00[AMR][1000 genomes]
rs59115933	0.84[AFR][1000 genomes]
rs60066089	1.00[AMR][1000 genomes]
rs61739271	1.00[AMR][1000 genomes]
rs7207425	1.00[AMR][1000 genomes]
rs7212939	0.84[AFR][1000 genomes]
rs7212941	1.00[AMR][1000 genomes]
rs7213607	1.00[AMR][1000 genomes]
rs7213652	1.00[AMR][1000 genomes]
rs7219055	1.00[AMR][1000 genomes]
rs7223319	1.00[AMR][1000 genomes]
rs7225251	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8067024	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8077553	0.86[ASW][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs9303447	1.00[AMR][1000 genomes]
rs9892156	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9892747	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9893569	1.00[AMR][1000 genomes]
rs9894800	1.00[AMR][1000 genomes]
rs9896244	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9897645	1.00[AMR][1000 genomes]
rs9897967	1.00[AMR][1000 genomes]
rs9897971	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9898853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9899420	1.00[AMR][1000 genomes]
rs9901535	1.00[AMR][1000 genomes]
rs9901665	1.00[AMR][1000 genomes]
rs9902352	1.00[AMR][1000 genomes]
rs9902447	1.00[AMR][1000 genomes]
rs9903376	1.00[AMR][1000 genomes]
rs9904939	0.80[AFR][1000 genomes]
rs9905071	1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs9910311	1.00[AMR][1000 genomes]
rs9910461	1.00[AMR][1000 genomes]
rs9910726	1.00[AMR][1000 genomes]
rs9911403	1.00[AMR][1000 genomes]
rs9912137	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9912417	1.00[AMR][1000 genomes]
rs9916169	0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
6	esv2489612	chr17:59823944-59825509	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59781600-59835400	Weak transcription	Hela-S3	cervix
2	chr17:59794400-59848200	Weak transcription	HUVEC	blood vessel
3	chr17:59804200-59847400	Weak transcription	K562	blood
4	chr17:59804600-59834200	Weak transcription	Osteobl	bone
5	chr17:59806200-59825600	Weak transcription	Thymus	Thymus
6	chr17:59807600-59838400	Weak transcription	Fetal Stomach	stomach
7	chr17:59811600-59825200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:59814000-59849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr17:59815000-59839200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:59815600-59828200	Weak transcription	NHLF	lung
11	chr17:59815600-59836000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr17:59815600-59844200	Weak transcription	HMEC	breast
13	chr17:59815800-59834400	Weak transcription	HSMM	muscle
14	chr17:59815800-59843400	Weak transcription	NHEK	skin
15	chr17:59816800-59887800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:59819000-59842600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr17:59819400-59843600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr17:59819400-59848200	Weak transcription	Primary B cells from cord blood	blood
19	chr17:59820000-59839200	Weak transcription	Fetal Muscle Leg	muscle
20	chr17:59820000-59841400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:59820000-59841400	Weak transcription	Ovary	ovary
22	chr17:59820000-59846600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:59820200-59825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:59820200-59825400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr17:59820200-59825400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr17:59820400-59825000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr17:59820400-59825200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:59820400-59835400	Weak transcription	Fetal Intestine Large	intestine
29	chr17:59820400-59840200	Weak transcription	Fetal Thymus	thymus
30	chr17:59820400-59877200	Weak transcription	NH-A	brain
31	chr17:59821400-59831600	Weak transcription	HepG2	liver
32	chr17:59821400-59834200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:59822800-59825000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:59823000-59827000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:59823200-59825200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr17:59823400-59827600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:59823600-59826000	ZNF genes & repeats	Dnd41	blood
38	chr17:59823800-59827600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr17:59824200-59825400	Weak transcription	Fetal Lung	lung
40	chr17:59824400-59826600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr17:59824400-59831800	Weak transcription	Primary T cells from cord blood	blood
42	chr17:59824400-59832000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:59824400-59839200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr17:59824600-59825400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr17:59824600-59825600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr17:59824600-59825800	Weak transcription	A549	lung

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