Variant report

Variant	rs9909882
Chromosome Location	chr17:59961513-59961514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59960457..59962339-chr20:55683260..55685106,2	MCF-7	breast:
2	chr17:59959753..59962989-chr17:60003686..60006854,4	MCF-7	breast:
3	chr17:59958225..59962598-chr20:55837947..55841825,4	MCF-7	breast:
4	chr17:59711762..59713818-chr17:59959330..59961568,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10401014	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10438772	0.81[AMR][1000 genomes]
rs16945750	1.00[EUR][1000 genomes]
rs16945766	1.00[MEX][hapmap]
rs2378907	1.00[MEX][hapmap]
rs28431006	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4988342	0.85[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs58025472	1.00[EUR][1000 genomes]
rs58046635	1.00[EUR][1000 genomes]
rs59794823	1.00[EUR][1000 genomes]
rs6504075	0.86[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6504076	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6504078	1.00[EUR][1000 genomes]
rs6504080	1.00[MEX][hapmap]
rs7211128	1.00[EUR][1000 genomes]
rs7212399	1.00[EUR][1000 genomes]
rs7212824	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7212884	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7213026	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7217530	1.00[EUR][1000 genomes]
rs7221827	1.00[EUR][1000 genomes]
rs7222876	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7224112	1.00[EUR][1000 genomes]
rs7226248	0.86[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73991952	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8065060	1.00[EUR][1000 genomes]
rs8068267	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069386	0.93[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069903	1.00[EUR][1000 genomes]
rs8069946	1.00[EUR][1000 genomes]
rs8078342	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8081200	0.87[ASW][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs9783841	1.00[EUR][1000 genomes]
rs9892063	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9892123	1.00[EUR][1000 genomes]
rs9894718	1.00[EUR][1000 genomes]
rs9896768	1.00[EUR][1000 genomes]
rs9899042	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9899780	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9902699	1.00[EUR][1000 genomes]
rs9903562	1.00[EUR][1000 genomes]
rs9905888	1.00[EUR][1000 genomes]
rs9909145	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9910067	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9910252	1.00[EUR][1000 genomes]
rs9910902	1.00[EUR][1000 genomes]
rs9913351	1.00[TSI][hapmap]
rs9914007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914605	1.00[EUR][1000 genomes]
rs9915023	1.00[EUR][1000 genomes]
rs9916070	1.00[TSI][hapmap]
rs9944467	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941200-59964600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:59941400-59965400	Weak transcription	Lung	lung
3	chr17:59941400-59975000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
6	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
7	chr17:59941600-59965200	Weak transcription	Psoas Muscle	Psoas
8	chr17:59941600-59965400	Weak transcription	Brain Substantia Nigra	brain
9	chr17:59941600-59965600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:59941600-59966800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:59941600-59979600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:59941600-59987600	Weak transcription	Right Ventricle	heart
13	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
14	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
15	chr17:59941800-59967000	Weak transcription	Fetal Brain Male	brain
16	chr17:59941800-59968800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr17:59941800-59969200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr17:59941800-59971800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:59941800-59979200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:59941800-59979200	Weak transcription	Brain Angular Gyrus	brain
21	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr17:59943600-59962200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:59944400-59962600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:59944400-59970000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr17:59944600-59962600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:59944600-59967600	Strong transcription	HepG2	liver
28	chr17:59946600-59989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr17:59947400-59977400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr17:59948000-59964000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr17:59948000-59965400	Weak transcription	Ovary	ovary
32	chr17:59948000-59972600	Weak transcription	NHDF-Ad	bronchial
33	chr17:59948000-59981800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr17:59948200-59980600	Weak transcription	HMEC	breast
35	chr17:59948200-59986800	Weak transcription	Fetal Kidney	kidney
36	chr17:59949200-59963600	Weak transcription	Fetal Lung	lung
37	chr17:59949200-59963800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr17:59949400-59963800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:59949400-59966800	Weak transcription	NH-A	brain
40	chr17:59949800-59963600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr17:59949800-59965600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:59949800-59966800	Weak transcription	K562	blood
43	chr17:59949800-59967000	Weak transcription	Colon Smooth Muscle	Colon
44	chr17:59950000-59979200	Weak transcription	NHLF	lung
45	chr17:59950800-59968800	Strong transcription	Adipose Nuclei	Adipose
46	chr17:59950800-59981600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:59951000-59962400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr17:59951000-59972400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr17:59951200-59962200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr17:59951400-59992200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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