Variant report

Variant	rs2475224
Chromosome Location	chr10:116243852-116243853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116235415..116237138-chr10:116243444..116246374,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11196753	0.81[AMR][1000 genomes]
rs11196758	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11196764	1.00[CEU][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11196766	1.00[CEU][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11196768	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs1923285	0.86[MEX][hapmap]
rs2145896	0.81[CHD][hapmap]
rs2475225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2475227	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2475230	0.83[MEX][hapmap]
rs2497679	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2497688	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2497706	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs34374858	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3802737	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7912323	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs941852	1.00[ASW][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9421175	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116194400-116251600	Weak transcription	Small Intestine	intestine
2	chr10:116199600-116244600	Weak transcription	A549	lung
3	chr10:116199800-116249200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:116214600-116263600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:116218400-116249200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:116222200-116264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:116225000-116267200	Weak transcription	Aorta	Aorta
8	chr10:116225600-116246800	Weak transcription	NHEK	skin
9	chr10:116225600-116278800	Weak transcription	HSMM	muscle
10	chr10:116227200-116247400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr10:116229400-116244800	Weak transcription	Thymus	Thymus
12	chr10:116231000-116244400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr10:116231200-116251600	Weak transcription	GM12878-XiMat	blood
14	chr10:116231400-116244400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:116231800-116244800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr10:116231800-116249200	Weak transcription	Pancreas	Pancrea
17	chr10:116232400-116246800	Weak transcription	HMEC	breast
18	chr10:116232600-116244600	Weak transcription	Colonic Mucosa	Colon
19	chr10:116232800-116244600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:116232800-116244800	Weak transcription	Hela-S3	cervix
21	chr10:116232800-116245600	Weak transcription	Brain Anterior Caudate	brain
22	chr10:116233000-116244600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr10:116233000-116247600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr10:116233000-116248800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr10:116233200-116245600	Weak transcription	HUVEC	blood vessel
26	chr10:116233800-116244400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:116234000-116247800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr10:116237200-116246200	Weak transcription	Brain Substantia Nigra	brain
29	chr10:116237400-116244400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:116237400-116248800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:116237800-116249000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr10:116238200-116244600	Strong transcription	Primary B cells from cord blood	blood
33	chr10:116238200-116245000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr10:116238200-116251400	Strong transcription	Primary B cells from peripheral blood	blood
35	chr10:116238400-116244200	Enhancers	Fetal Heart	heart
36	chr10:116238400-116251600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:116238600-116249200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:116239000-116248800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr10:116239400-116244600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr10:116239400-116244600	Weak transcription	Gastric	stomach
41	chr10:116239400-116246600	Weak transcription	Fetal Kidney	kidney
42	chr10:116239400-116249200	Weak transcription	Stomach Mucosa	stomach
43	chr10:116239400-116249400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr10:116240000-116246800	Strong transcription	HepG2	liver
45	chr10:116240400-116248400	Strong transcription	Liver	Liver
46	chr10:116240600-116250400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr10:116240800-116247000	Strong transcription	Esophagus	oesophagus
48	chr10:116241000-116244800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr10:116241200-116244800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr10:116241400-116244000	Enhancers	Fetal Lung	lung

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