Variant report

Variant	rs17163450
Chromosome Location	chr1:222894848-222894849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222885159..222888489-chr1:222893154..222895532,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186063	Chromatin interaction
ENSG00000162819	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495196	0.84[ASW][hapmap];0.94[MEX][hapmap]
rs11485123	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs1391558	0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs17011686	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17163219	0.84[ASW][hapmap]
rs17163337	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs17163453	0.84[ASW][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17163468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2030076	0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs2088514	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2133188	0.81[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs2378604	0.98[ASN][1000 genomes]
rs2936020	0.83[ASN][1000 genomes]
rs2936023	0.83[ASN][1000 genomes]
rs2936049	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.92[ASN][1000 genomes]
rs3002129	0.88[ASN][1000 genomes]
rs3002148	0.83[ASN][1000 genomes]
rs3008625	0.83[ASN][1000 genomes]
rs3008629	0.86[ASN][1000 genomes]
rs3008637	0.92[ASN][1000 genomes]
rs34433664	0.96[ASN][1000 genomes]
rs35507977	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs3811465	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs4846773	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 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	chr1:222887200-222899000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:222887200-222899000	Weak transcription	Esophagus	oesophagus
3	chr1:222887200-222909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:222887400-222895200	Weak transcription	Psoas Muscle	Psoas
5	chr1:222887400-222902200	Weak transcription	Fetal Heart	heart
6	chr1:222887400-222903600	Weak transcription	Aorta	Aorta
7	chr1:222887400-222904400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:222887400-222908800	Weak transcription	Stomach Mucosa	stomach
9	chr1:222887400-222909600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:222887400-222912000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:222887600-222895600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:222887600-222896600	Weak transcription	Right Ventricle	heart
13	chr1:222887600-222903200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:222887600-222912400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:222888000-222909200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:222888200-222895200	Weak transcription	Left Ventricle	heart
17	chr1:222888200-222896600	Weak transcription	Pancreas	Pancrea
18	chr1:222888200-222899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:222888200-222899000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:222888200-222899800	Weak transcription	Gastric	stomach
21	chr1:222888200-222900000	Weak transcription	Fetal Brain Male	brain
22	chr1:222888200-222909200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:222888200-222909600	Weak transcription	Spleen	Spleen
24	chr1:222888200-222910200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:222888200-222910400	Strong transcription	Fetal Thymus	thymus
26	chr1:222888400-222905200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:222888400-222905600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:222888400-222907800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:222888400-222908200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:222888400-222908600	Strong transcription	HSMM	muscle
31	chr1:222888400-222908600	Strong transcription	NHDF-Ad	bronchial
32	chr1:222888400-222909600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:222888400-222909600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:222888400-222910000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:222888400-222910000	Strong transcription	Fetal Intestine Large	intestine
36	chr1:222888400-222910200	Strong transcription	Placenta	Placenta
37	chr1:222888400-222910800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:222888600-222895200	Weak transcription	Small Intestine	intestine
39	chr1:222888600-222897600	Weak transcription	Thymus	Thymus
40	chr1:222888600-222908400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:222888600-222909800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:222888600-222910400	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr1:222888600-222910800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:222888600-222911200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:222888600-222911400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:222888800-222902200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:222888800-222908800	Strong transcription	Dnd41	blood
48	chr1:222889000-222902800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:222889000-222905400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:222889000-222908200	Strong transcription	NH-A	brain

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