Variant report

Variant	rs1028347
Chromosome Location	chr6:25366699-25366700
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	chr6:25360833..25363264-chr6:25364832..25366836,2	MCF-7	breast:
2	chr6:25366098..25368844-chr6:25396135..25397777,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1013045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209305	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12173289	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12210416	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs13211247	0.83[ASN][1000 genomes]
rs13217807	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1556043	0.83[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs169978	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs177333	0.85[ASN][1000 genomes]
rs215009	0.89[ASN][1000 genomes]
rs215013	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs215014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2744234	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2744237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35361710	0.85[ASN][1000 genomes]
rs4712921	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712922	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6913927	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6933921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs760864	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7760906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
2	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
3	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
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv601168	chr6:25346334-25393306	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 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	chr6:25359800-25367200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:25360000-25367200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:25360000-25367400	Weak transcription	Lung	lung
4	chr6:25360000-25367400	Weak transcription	Right Atrium	heart
5	chr6:25360400-25367600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:25360400-25367600	Weak transcription	Pancreas	Pancrea
7	chr6:25360400-25367800	Weak transcription	Brain Germinal Matrix	brain
8	chr6:25360400-25369200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:25360800-25367200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr6:25360800-25367600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:25360800-25369800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:25361000-25367000	Weak transcription	Fetal Intestine Small	intestine
13	chr6:25361000-25367200	Weak transcription	Fetal Intestine Large	intestine
14	chr6:25361000-25367200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:25361000-25367400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:25361000-25369200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:25361000-25369400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr6:25361000-25369400	Weak transcription	Left Ventricle	heart
19	chr6:25361000-25369800	Weak transcription	Brain Substantia Nigra	brain
20	chr6:25361200-25367200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:25362000-25367000	Weak transcription	NHLF	lung
22	chr6:25362000-25367200	Weak transcription	Brain Anterior Caudate	brain
23	chr6:25362600-25367200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:25362800-25367600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:25363400-25367200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:25363800-25367000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:25363800-25367400	Weak transcription	Fetal Lung	lung
28	chr6:25364000-25367200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:25364000-25367200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:25364000-25367200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:25364200-25367200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:25364400-25367000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:25364400-25367000	Weak transcription	Adipose Nuclei	Adipose
34	chr6:25364400-25367200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:25364800-25367000	Enhancers	Fetal Thymus	thymus
36	chr6:25365200-25367200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr6:25365400-25366800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr6:25365400-25367000	Enhancers	Thymus	Thymus
39	chr6:25365400-25367200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:25365600-25367000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr6:25365800-25367200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr6:25365800-25369200	Weak transcription	Fetal Brain Female	brain
43	chr6:25366000-25367000	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:25366000-25367200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:25366000-25367400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr6:25366000-25367400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr6:25366200-25366800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:25366200-25367200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:25366200-25367200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr6:25366200-25367800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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