Variant report

Variant	rs2744293
Chromosome Location	chr6:25295258-25295259
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	chr6:25288747..25291060-chr6:25294268..25296808,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs2018839	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2064206	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2143022	0.85[CEU][hapmap]
rs2690041	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690117	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2690118	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2690132	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690134	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690135	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744288	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744289	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744294	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744297	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744299	0.85[CEU][hapmap]
rs2744300	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25281200-25296000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:25281400-25295800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:25281400-25295800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:25281400-25295800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:25281400-25296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:25281600-25295600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:25281600-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:25281600-25295800	Weak transcription	Thymus	Thymus
10	chr6:25281600-25296000	Weak transcription	Primary T cells from cord blood	blood
11	chr6:25281600-25296000	Weak transcription	Fetal Thymus	thymus
12	chr6:25281600-25296400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:25281800-25295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:25282800-25296400	Weak transcription	Hela-S3	cervix
15	chr6:25286800-25300800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:25287800-25296000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:25288600-25295400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr6:25288600-25296000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:25288600-25296400	Weak transcription	Gastric	stomach
20	chr6:25288600-25301200	Weak transcription	Brain Anterior Caudate	brain
21	chr6:25289000-25295800	Weak transcription	Esophagus	oesophagus
22	chr6:25289000-25298600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:25289000-25300600	Weak transcription	Pancreas	Pancrea
24	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:25291000-25295600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:25291000-25296000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:25291000-25296000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:25291200-25295800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:25291200-25295800	Weak transcription	Fetal Intestine Large	intestine
30	chr6:25291200-25295800	Weak transcription	Right Atrium	heart
31	chr6:25291200-25296400	Weak transcription	Left Ventricle	heart
32	chr6:25291800-25296600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:25292200-25303000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:25292400-25301000	Weak transcription	Adipose Nuclei	Adipose
35	chr6:25292600-25295600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:25292600-25295800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:25292600-25296000	Weak transcription	Fetal Lung	lung
38	chr6:25292800-25295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:25292800-25295800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:25292800-25295800	Weak transcription	NHEK	skin
41	chr6:25292800-25296400	Weak transcription	Brain Angular Gyrus	brain
42	chr6:25293000-25295800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:25293000-25295800	Weak transcription	HMEC	breast
44	chr6:25293000-25301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:25293200-25301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:25293800-25298000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:25294200-25295800	Weak transcription	Fetal Intestine Small	intestine
48	chr6:25294200-25311200	Weak transcription	Lung	lung
49	chr6:25294400-25297000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr6:25294600-25295400	Enhancers	Small Intestine	intestine

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