Variant report

Variant	rs17532708
Chromosome Location	chr1:222899427-222899428
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	chr1:222899320..222901092-chr1:222902365..222904484,2	K562	blood:
2	chr1:222895272..222897117-chr1:222898129..222900619,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1133220	0.87[ASN][1000 genomes]
rs12043288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138316	0.88[ASN][1000 genomes]
rs12749296	0.90[EUR][1000 genomes]
rs17011666	0.82[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17011681	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs17163313	0.83[ASN][1000 genomes]
rs17163345	0.84[ASN][1000 genomes]
rs17163358	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs17163360	0.84[ASN][1000 genomes]
rs17163363	0.85[ASN][1000 genomes]
rs17465637	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs17465940	0.81[ASN][1000 genomes]
rs17465982	0.82[ASN][1000 genomes]
rs1909195	0.81[ASN][1000 genomes]
rs2068814	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2133187	0.84[ASN][1000 genomes]
rs2133189	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2270707	0.87[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2291832	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2291834	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2378603	0.87[EUR][1000 genomes]
rs2378607	0.93[EUR][1000 genomes]
rs28521319	0.80[EUR][1000 genomes]
rs28654270	0.87[EUR][1000 genomes]
rs28765200	0.86[EUR][1000 genomes]
rs34032254	0.92[ASN][1000 genomes]
rs34885880	0.91[EUR][1000 genomes]
rs35158675	0.83[ASN][1000 genomes]
rs35175385	0.92[ASN][1000 genomes]
rs35300015	0.87[EUR][1000 genomes]
rs35626308	0.83[ASN][1000 genomes]
rs35700460	0.84[ASN][1000 genomes]
rs35725247	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748626	0.83[ASN][1000 genomes]
rs4282830	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575092	0.87[ASN][1000 genomes]
rs4846384	0.82[ASN][1000 genomes]
rs61824331	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61825253	0.88[EUR][1000 genomes]
rs61825254	0.87[EUR][1000 genomes]
rs61825258	0.84[EUR][1000 genomes]
rs61825259	0.88[EUR][1000 genomes]
rs6700083	0.86[EUR][1000 genomes]
rs67180937	0.85[ASN][1000 genomes]
rs71524942	0.96[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17532708	TGFB2	cis	cerebellum	SCAN
rs17532708	HHIPL2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222887200-222909600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:222887400-222902200	Weak transcription	Fetal Heart	heart
3	chr1:222887400-222903600	Weak transcription	Aorta	Aorta
4	chr1:222887400-222904400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:222887400-222908800	Weak transcription	Stomach Mucosa	stomach
6	chr1:222887400-222909600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:222887400-222912000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:222887600-222903200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:222887600-222912400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:222888000-222909200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:222888200-222899800	Weak transcription	Gastric	stomach
12	chr1:222888200-222900000	Weak transcription	Fetal Brain Male	brain
13	chr1:222888200-222909200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:222888200-222909600	Weak transcription	Spleen	Spleen
15	chr1:222888200-222910200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:222888200-222910400	Strong transcription	Fetal Thymus	thymus
17	chr1:222888400-222905200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:222888400-222905600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:222888400-222907800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:222888400-222908200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:222888400-222908600	Strong transcription	HSMM	muscle
22	chr1:222888400-222908600	Strong transcription	NHDF-Ad	bronchial
23	chr1:222888400-222909600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:222888400-222909600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:222888400-222910000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:222888400-222910000	Strong transcription	Fetal Intestine Large	intestine
27	chr1:222888400-222910200	Strong transcription	Placenta	Placenta
28	chr1:222888400-222910800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:222888600-222908400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:222888600-222909800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:222888600-222910400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:222888600-222910800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:222888600-222911200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:222888600-222911400	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:222888800-222902200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:222888800-222908800	Strong transcription	Dnd41	blood
37	chr1:222889000-222902800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:222889000-222905400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:222889000-222908200	Strong transcription	NH-A	brain
40	chr1:222889000-222910000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:222889000-222910200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:222889000-222911200	Strong transcription	Liver	Liver
43	chr1:222889000-222911400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:222889200-222910000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:222889200-222910600	Strong transcription	Adipose Nuclei	Adipose
46	chr1:222889600-222905000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:222889600-222906000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:222889600-222908200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:222889600-222909400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:222889800-222909200	Strong transcription	Rectal Mucosa Donor 31	rectum

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