Variant report

Variant	rs12207259
Chromosome Location	chr6:151034267-151034268
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	chr6:151031833..151034692-chr6:151036440..151039323,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2279629	0.80[CEU][hapmap]
rs4869940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6557084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6557085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6557086	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7761077	0.89[AFR][1000 genomes]
rs7769973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9371193	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9371194	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs9478788	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3439835	chr6:151027582-151036981	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1019919	chr6:151028969-151161789	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv538474	chr6:151028969-151161789	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:151019000-151035200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:151021600-151040600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:151026800-151043600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:151029400-151041800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr6:151032200-151037600	Weak transcription	Gastric	stomach
6	chr6:151032800-151034400	Enhancers	Liver	Liver
7	chr6:151032800-151036600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:151033000-151035000	Enhancers	Spleen	Spleen
9	chr6:151033000-151035200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:151033000-151035600	Enhancers	Fetal Lung	lung
11	chr6:151033000-151035800	Enhancers	Brain Substantia Nigra	brain
12	chr6:151033000-151035800	Enhancers	Fetal Heart	heart
13	chr6:151033000-151036200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:151033200-151034400	Enhancers	Brain Germinal Matrix	brain
15	chr6:151033200-151034400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr6:151033200-151035000	Enhancers	Left Ventricle	heart
17	chr6:151033200-151035400	Enhancers	Right Atrium	heart
18	chr6:151033200-151035800	Enhancers	Fetal Kidney	kidney
19	chr6:151033200-151036000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:151033200-151036000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:151033200-151036000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:151033200-151036200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:151033400-151034400	Enhancers	Thymus	Thymus
24	chr6:151033400-151034600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:151033400-151034800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:151033400-151038000	Weak transcription	Esophagus	oesophagus
27	chr6:151033600-151035000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr6:151033600-151035400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:151033600-151035600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:151033600-151037600	Weak transcription	Pancreas	Pancrea
31	chr6:151033600-151038000	Weak transcription	Primary B cells from cord blood	blood
32	chr6:151033600-151038200	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:151033600-151040200	Weak transcription	Fetal Stomach	stomach
34	chr6:151033600-151042000	Weak transcription	Fetal Intestine Small	intestine
35	chr6:151033600-151050200	Weak transcription	Lung	lung
36	chr6:151033800-151034400	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr6:151033800-151035000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr6:151033800-151035400	Enhancers	Placenta	Placenta
39	chr6:151034000-151034600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr6:151034000-151034800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr6:151034000-151034800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:151034000-151035200	Enhancers	Brain Anterior Caudate	brain
43	chr6:151034000-151035400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:151034000-151035600	Enhancers	Brain Hippocampus Middle	brain
45	chr6:151034000-151040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:151034200-151034800	Weak transcription	Fetal Thymus	thymus
47	chr6:151034200-151035000	Enhancers	Fetal Brain Female	brain
48	chr6:151034200-151035000	Enhancers	Right Ventricle	heart
49	chr6:151034200-151035800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:151034200-151037600	Weak transcription	Rectal Mucosa Donor 31	rectum

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