Variant report

Variant	rs2247528
Chromosome Location	chr10:116307504-116307505
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	chr10:116062527..116065028-chr10:116306481..116309077,3	MCF-7	breast:
2	chr10:116065949..116067455-chr10:116305954..116308576,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169129	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10160023	0.81[ASN][1000 genomes]
rs10749169	0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10749170	0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10885572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10885573	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10885575	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10885580	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11196779	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196780	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196781	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196785	0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12569428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2145894	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247624	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2475239	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2475240	0.87[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2475241	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2475242	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483531	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483564	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2483571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483577	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2483579	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483580	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2483584	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2483585	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483588	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483599	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483612	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497708	0.80[JPT][hapmap]
rs2497710	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2497712	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497717	0.85[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2497719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2497720	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497721	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497722	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2497723	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35078486	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4144582	0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4514325	0.88[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4568918	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56001223	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56086836	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56339171	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7094292	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs867736	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883511	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9421179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116287400-116310600	Weak transcription	Brain Angular Gyrus	brain
2	chr10:116287400-116310600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:116297600-116308600	Enhancers	Primary B cells from peripheral blood	blood
4	chr10:116297800-116308600	Enhancers	Stomach Mucosa	stomach
5	chr10:116298000-116308800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:116298200-116307800	Strong transcription	Fetal Intestine Small	intestine
7	chr10:116298400-116307600	Weak transcription	Brain Substantia Nigra	brain
8	chr10:116298400-116310200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:116298600-116311600	Weak transcription	Gastric	stomach
10	chr10:116298800-116310400	Weak transcription	Small Intestine	intestine
11	chr10:116298800-116310600	Weak transcription	Colonic Mucosa	Colon
12	chr10:116299600-116308200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:116299800-116308800	Genic enhancers	Left Ventricle	heart
14	chr10:116300400-116307600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:116300600-116310600	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:116301800-116310600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr10:116301800-116310600	Weak transcription	Fetal Lung	lung
18	chr10:116301800-116310800	Weak transcription	HSMM	muscle
19	chr10:116303800-116307600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:116304000-116307800	Strong transcription	Right Ventricle	heart
21	chr10:116304000-116310600	Weak transcription	Brain Anterior Caudate	brain
22	chr10:116304000-116310600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:116304200-116307600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:116304200-116308800	Enhancers	Fetal Thymus	thymus
25	chr10:116304200-116310800	Weak transcription	Pancreas	Pancrea
26	chr10:116304400-116308400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr10:116304400-116308800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr10:116304600-116308800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr10:116304600-116308800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr10:116304800-116308200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr10:116304800-116308400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr10:116304800-116308400	Enhancers	Thymus	Thymus
33	chr10:116304800-116308800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr10:116305000-116308400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr10:116305000-116311000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr10:116305000-116317600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr10:116305200-116308200	Weak transcription	HepG2	liver
38	chr10:116305200-116308400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr10:116305200-116308800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr10:116305200-116308800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr10:116305200-116310600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:116305200-116310600	Weak transcription	Fetal Muscle Leg	muscle
43	chr10:116305200-116310800	Weak transcription	Esophagus	oesophagus
44	chr10:116305200-116310800	Weak transcription	Lung	lung
45	chr10:116305200-116316000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr10:116305200-116318200	Weak transcription	Fetal Intestine Large	intestine
47	chr10:116305400-116308200	Weak transcription	HMEC	breast
48	chr10:116305600-116308200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr10:116306000-116307600	Strong transcription	HSMMtube	muscle
50	chr10:116306400-116308800	Enhancers	Primary T cells from cord blood	blood

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