Variant report

Variant	rs2475225
Chromosome Location	chr10:116244880-116244881
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	chr10:116235415..116237138-chr10:116243444..116246374,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11196753	0.81[AMR][1000 genomes]
rs11196758	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11196764	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11196766	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196768	0.88[AMR][1000 genomes]
rs2475224	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];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2497679	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2497688	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2497702	0.84[ASN][1000 genomes]
rs34374858	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3802737	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7912323	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs941852	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9421175	0.88[AMR][1000 genomes];0.96[EUR][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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116194400-116251600	Weak transcription	Small Intestine	intestine
2	chr10:116199800-116249200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr10:116214600-116263600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:116218400-116249200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr10:116222200-116264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr10:116225000-116267200	Weak transcription	Aorta	Aorta
7	chr10:116225600-116246800	Weak transcription	NHEK	skin
8	chr10:116225600-116278800	Weak transcription	HSMM	muscle
9	chr10:116227200-116247400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:116231200-116251600	Weak transcription	GM12878-XiMat	blood
11	chr10:116231800-116249200	Weak transcription	Pancreas	Pancrea
12	chr10:116232400-116246800	Weak transcription	HMEC	breast
13	chr10:116232800-116245600	Weak transcription	Brain Anterior Caudate	brain
14	chr10:116233000-116247600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr10:116233000-116248800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr10:116233200-116245600	Weak transcription	HUVEC	blood vessel
17	chr10:116234000-116247800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr10:116237200-116246200	Weak transcription	Brain Substantia Nigra	brain
19	chr10:116237400-116248800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr10:116237800-116249000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr10:116238200-116245000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr10:116238200-116251400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr10:116238400-116251600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr10:116238600-116249200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:116239000-116248800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:116239400-116246600	Weak transcription	Fetal Kidney	kidney
27	chr10:116239400-116249200	Weak transcription	Stomach Mucosa	stomach
28	chr10:116239400-116249400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr10:116240000-116246800	Strong transcription	HepG2	liver
30	chr10:116240400-116248400	Strong transcription	Liver	Liver
31	chr10:116240600-116250400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:116240800-116247000	Strong transcription	Esophagus	oesophagus
33	chr10:116241800-116251600	Strong transcription	HSMMtube	muscle
34	chr10:116242000-116247800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr10:116242400-116245800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr10:116242400-116246200	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr10:116242400-116248000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr10:116242400-116250000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr10:116242800-116245000	Enhancers	Right Atrium	heart
40	chr10:116242800-116249000	Strong transcription	Primary T cells from cord blood	blood
41	chr10:116243000-116246000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:116243000-116286200	Weak transcription	Spleen	Spleen
43	chr10:116243200-116247800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:116243200-116249200	Weak transcription	Brain Angular Gyrus	brain
45	chr10:116243400-116248000	Strong transcription	Fetal Intestine Large	intestine
46	chr10:116243400-116251200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:116243400-116251600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr10:116243600-116245800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr10:116243600-116245800	Genic enhancers	Right Ventricle	heart
50	chr10:116243600-116246800	Strong transcription	Fetal Thymus	thymus

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