Variant report

Variant	rs17008565
Chromosome Location	chr2:73228068-73228069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73212585..73213121-chr2:73228063..73228815,2	MCF-7	breast:
2	chr2:73227713..73230641-chr2:73231443..73233674,2	K562	blood:
3	chr2:73227183..73229213-chr2:73231275..73232943,2	K562	blood:
4	chr2:73218918..73222719-chr2:73226745..73229455,3	K562	blood:

Variant related genes	Relation type
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1046183	0.85[JPT][hapmap]
rs10496188	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13404068	0.91[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs17008541	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17008579	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17008608	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2421099	0.91[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs3849393	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58731407	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59108557	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs61164794	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61652727	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62147718	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62147722	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62147726	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62147727	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62147728	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62147731	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62147733	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62147735	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62147756	0.82[EUR][1000 genomes]
rs62148129	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62148130	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66570372	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6710911	0.90[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753054	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753133	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753301	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67673165	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73183200-73228200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:73190600-73234400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:73194200-73248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:73207800-73263200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:73208000-73247600	Weak transcription	Primary B cells from cord blood	blood
6	chr2:73211000-73258400	Weak transcription	Colonic Mucosa	Colon
7	chr2:73211600-73235800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:73212200-73247400	Weak transcription	HSMMtube	muscle
9	chr2:73212400-73236000	Weak transcription	Esophagus	oesophagus
10	chr2:73212800-73238800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:73213800-73236200	Weak transcription	Pancreas	Pancrea
12	chr2:73214000-73232000	Weak transcription	Aorta	Aorta
13	chr2:73214000-73238400	Weak transcription	Fetal Lung	lung
14	chr2:73214200-73247800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
16	chr2:73215200-73228400	Weak transcription	Placenta	Placenta
17	chr2:73215400-73236000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:73215800-73235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:73215800-73247400	Weak transcription	Thymus	Thymus
20	chr2:73215800-73263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:73216000-73236000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:73216200-73248800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr2:73216800-73234400	Weak transcription	Primary T cells from cord blood	blood
24	chr2:73217400-73231800	Weak transcription	Fetal Heart	heart
25	chr2:73217400-73236200	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:73217400-73249000	Weak transcription	Ovary	ovary
27	chr2:73217800-73237400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:73220600-73249000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:73220600-73263200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:73220800-73228800	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:73221200-73231400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:73221200-73263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:73222200-73229000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr2:73222400-73228400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr2:73222600-73228800	Strong transcription	Fetal Stomach	stomach
36	chr2:73223000-73228600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:73223000-73229200	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:73223200-73229600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:73223200-73274600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:73223400-73232200	Weak transcription	Fetal Brain Female	brain
41	chr2:73223400-73232800	Weak transcription	Brain Germinal Matrix	brain
42	chr2:73223600-73232400	Weak transcription	Brain Angular Gyrus	brain
43	chr2:73223600-73235400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:73224600-73261200	Weak transcription	Brain Substantia Nigra	brain
45	chr2:73225000-73228400	Strong transcription	Right Ventricle	heart
46	chr2:73225400-73228400	Enhancers	Liver	Liver
47	chr2:73225400-73228600	Strong transcription	Lung	lung
48	chr2:73225400-73229000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:73226200-73236200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:73226200-73248800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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