Variant report

Variant	rs1012502
Chromosome Location	chr6:11365491-11365492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11363261..11366684-chr6:11366769..11368460,3	MCF-7	breast:
2	chr6:11358576..11361790-chr6:11363070..11366053,4	MCF-7	breast:
3	chr6:11355836..11357922-chr6:11365325..11366984,2	MCF-7	breast:
4	chr6:11231312..11234053-chr6:11364162..11365969,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1013678	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947204	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12193099	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12199545	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12204242	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208626	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12210644	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12215372	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12215715	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215894	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13198555	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13217274	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1810451	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3798752	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4276494	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4533978	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4632886	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4711271	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711272	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5019594	0.83[CHB][hapmap]
rs6916534	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6918440	0.83[CHB][hapmap]
rs6932496	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7738560	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7768351	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9296000	0.82[CHB][hapmap]
rs9348868	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357127	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461714	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9469034	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11355000-11367400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:11355200-11370800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:11357200-11371200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:11357600-11365600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:11357600-11367600	Weak transcription	Aorta	Aorta
6	chr6:11357800-11366600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:11357800-11370400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr6:11358000-11367800	Weak transcription	Small Intestine	intestine
9	chr6:11358200-11367400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:11358800-11366400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:11358800-11367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:11359400-11369800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:11359600-11366400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr6:11360000-11366400	Weak transcription	Esophagus	oesophagus
15	chr6:11360200-11366800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:11361000-11366400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:11361200-11365800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
18	chr6:11361200-11366800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:11361200-11370600	Weak transcription	Thymus	Thymus
20	chr6:11361600-11367200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:11362600-11366400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:11362800-11365600	Enhancers	HMEC	breast
23	chr6:11362800-11366800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:11363800-11367400	Enhancers	HepG2	liver
25	chr6:11364200-11365600	Enhancers	Stomach Mucosa	stomach
26	chr6:11364200-11365800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:11364200-11366000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:11364200-11366000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr6:11364200-11366800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr6:11364400-11366000	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr6:11364400-11366400	Weak transcription	Pancreas	Pancrea
32	chr6:11364600-11366800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:11364600-11369400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr6:11364600-11371200	Enhancers	HUVEC	blood vessel
35	chr6:11364600-11381200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr6:11364800-11365600	Enhancers	Primary hematopoietic stem cells	blood
37	chr6:11364800-11366000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:11364800-11366200	Enhancers	Liver	Liver
39	chr6:11364800-11370400	Weak transcription	Spleen	Spleen
40	chr6:11364800-11370800	Weak transcription	Placenta	Placenta
41	chr6:11365000-11365800	Genic enhancers	GM12878-XiMat	blood
42	chr6:11365000-11366000	Genic enhancers	Primary B cells from cord blood	blood
43	chr6:11365000-11366000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr6:11365000-11366800	Weak transcription	NHEK	skin
45	chr6:11365000-11370600	Weak transcription	Fetal Thymus	thymus
46	chr6:11365200-11365600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:11365200-11366800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:11365200-11367000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:11365200-11367000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:11365400-11365600	Enhancers	A549	lung

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