Variant report

Variant	rs12450995
Chromosome Location	chr17:60058418-60058419
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:60056360..60059344-chr17:60060297..60063988,4	MCF-7	breast:
2	chr17:60019206..60021489-chr17:60057845..60060519,2	MCF-7	breast:
3	chr17:60058379..60061506-chr17:60139954..60143390,3	MCF-7	breast:
4	chr17:60052402..60054800-chr17:60057240..60059502,2	K562	blood:
5	chr17:60003275..60005722-chr17:60057726..60059671,3	MCF-7	breast:
6	chr17:60044075..60048117-chr17:60057244..60060340,4	MCF-7	breast:
7	chr17:60057894..60059644-chr17:60062477..60064261,2	K562	blood:
8	chr17:60055995..60057955-chr17:60058135..60059937,2	MCF-7	breast:
9	chr17:60050203..60052259-chr17:60057638..60059611,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11079464	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs28610444	0.85[AMR][1000 genomes]
rs28755966	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968410	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4968466	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4968473	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4968477	0.93[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs6504077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6504079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7207930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7210061	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7218545	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7222262	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8072101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8081805	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8081812	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs9747976	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9889324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9889676	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs9901321	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9902812	0.92[CEU][hapmap]
rs9908352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9913443	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60018000-60072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr17:60018000-60073400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:60018600-60072600	Strong transcription	Fetal Thymus	thymus
4	chr17:60018800-60073600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:60020400-60073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:60020600-60073000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr17:60020800-60073800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:60021200-60097000	Strong transcription	Dnd41	blood
9	chr17:60021800-60073600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr17:60025400-60074200	Strong transcription	Liver	Liver
11	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr17:60028400-60059600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:60032800-60058600	Weak transcription	Fetal Heart	heart
14	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
15	chr17:60034800-60072800	Strong transcription	Placenta	Placenta
16	chr17:60035800-60064400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr17:60036000-60074000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:60036400-60070000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr17:60038400-60059400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:60040400-60058800	Weak transcription	NHEK	skin
21	chr17:60042600-60063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:60042800-60058600	Weak transcription	Brain Substantia Nigra	brain
23	chr17:60042800-60059600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr17:60042800-60059600	Weak transcription	Pancreas	Pancrea
25	chr17:60042800-60059800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr17:60042800-60105200	Weak transcription	Psoas Muscle	Psoas
27	chr17:60043200-60059400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr17:60044000-60058800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr17:60044000-60059400	Weak transcription	Fetal Brain Male	brain
30	chr17:60044400-60062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:60044800-60059200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr17:60045600-60059600	Weak transcription	Brain Angular Gyrus	brain
33	chr17:60046400-60062800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr17:60047200-60058600	Weak transcription	Gastric	stomach
35	chr17:60047600-60058600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr17:60047800-60058800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr17:60048000-60058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:60048000-60062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr17:60048400-60059600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr17:60048400-60072800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr17:60048600-60074200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr17:60048800-60097600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr17:60049400-60060000	Weak transcription	Aorta	Aorta
44	chr17:60050000-60058600	Weak transcription	Colonic Mucosa	Colon
45	chr17:60050200-60100800	Weak transcription	Small Intestine	intestine
46	chr17:60050400-60058600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr17:60050400-60058800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr17:60050600-60058600	Weak transcription	Hela-S3	cervix
49	chr17:60050600-60058800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr17:60050600-60059200	Weak transcription	NHLF	lung

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