Variant report

Variant	rs12106682
Chromosome Location	chr3:150888373-150888374
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150886462..150889127-chr3:150925386..150928089,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12631155	0.89[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs1431494	0.89[ASW][hapmap]
rs16863173	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16863204	1.00[ASW][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs16863219	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863227	0.88[YRI][hapmap];0.89[AFR][1000 genomes]
rs16863229	0.89[ASW][hapmap]
rs16863248	0.89[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs16863250	1.00[EUR][1000 genomes]
rs2870413	0.89[ASW][hapmap];0.94[MKK][hapmap];0.83[YRI][hapmap]
rs2870415	0.89[ASW][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs3773614	0.89[ASW][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap]
rs3821666	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs3960212	1.00[EUR][1000 genomes]
rs41526246	0.89[ASW][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41526349	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58321514	1.00[EUR][1000 genomes]
rs60620665	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60816259	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60966250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6440723	0.89[ASW][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs6440725	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6767615	1.00[EUR][1000 genomes]
rs6774659	1.00[EUR][1000 genomes]
rs6776934	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6777211	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6787551	1.00[EUR][1000 genomes]
rs6790244	1.00[EUR][1000 genomes]
rs6790349	1.00[EUR][1000 genomes]
rs6794447	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73009177	1.00[EUR][1000 genomes]
rs73012977	1.00[EUR][1000 genomes]
rs73012978	1.00[EUR][1000 genomes]
rs73012986	1.00[EUR][1000 genomes]
rs73012988	1.00[EUR][1000 genomes]
rs73012992	1.00[EUR][1000 genomes]
rs73013000	1.00[EUR][1000 genomes]
rs73014806	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73014871	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73014873	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73016712	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73016789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73018620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73019093	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73019099	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73021108	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73021116	1.00[EUR][1000 genomes]
rs73021129	1.00[EUR][1000 genomes]
rs73021144	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7618087	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7638986	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7653225	0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150863200-150889000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:150871200-150888400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:150872800-150910800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:150873200-150888800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:150873200-150910200	Weak transcription	Brain Angular Gyrus	brain
6	chr3:150873600-150889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:150873800-150890000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:150873800-150890000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:150873800-150913800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:150874200-150888600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:150874200-150888800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:150874200-150896000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:150874600-150888400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:150874600-150889200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:150874800-150900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:150877600-150888800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:150878000-150888400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
19	chr3:150878400-150888800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:150878400-150890800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:150880400-150900200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:150880800-150900400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:150883400-150889000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:150883800-150896000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:150884200-150888400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:150884200-150906600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:150884400-150893400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:150886000-150890800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:150886200-150889800	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:150886200-150890400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:150886200-150890400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr3:150886200-150890400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:150886200-150890800	Enhancers	Primary hematopoietic stem cells	blood
34	chr3:150886200-150890800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:150886200-150892400	Enhancers	Primary T cells from cord blood	blood
36	chr3:150886200-150893000	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:150886600-150888600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:150886600-150890200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr3:150886600-150890400	Enhancers	Fetal Thymus	thymus
40	chr3:150886800-150892600	Weak transcription	Liver	Liver
41	chr3:150887000-150889200	Enhancers	Fetal Muscle Leg	muscle
42	chr3:150887200-150888400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:150887200-150888600	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:150887200-150888600	Enhancers	Stomach Mucosa	stomach
45	chr3:150887200-150889000	Enhancers	Dnd41	blood
46	chr3:150887200-150889200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr3:150887400-150888400	Weak transcription	Adipose Nuclei	Adipose
48	chr3:150887600-150888400	Enhancers	Small Intestine	intestine
49	chr3:150887600-150888800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:150887600-150889000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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