Variant report

Variant	rs1013678
Chromosome Location	chr6:11364205-11364206
allele	A/C/G/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	chr6:11363308..11365287-chr6:11389526..11391473,2	MCF-7	breast:
3	chr6:11345079..11346896-chr6:11363050..11365250,2	K562	blood:
4	chr6:11358576..11361790-chr6:11363070..11366053,4	MCF-7	breast:
5	chr6:11339887..11342299-chr6:11361648..11364583,2	MCF-7	breast:
6	chr6:11231312..11234053-chr6:11364162..11365969,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1012502	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	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193099	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12199545	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12204242	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12208626	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210644	0.80[ASN][1000 genomes]
rs12215372	0.87[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12215715	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215894	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13198555	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13217274	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1810451	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2179178	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3798752	0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4276494	0.81[ASN][1000 genomes]
rs4533978	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4632886	0.80[ASN][1000 genomes]
rs4711271	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4711272	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5019594	0.83[CHB][hapmap]
rs6916534	0.82[ASN][1000 genomes]
rs6918440	0.83[CHB][hapmap]
rs6932496	0.87[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7738560	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7768351	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296000	0.82[CHB][hapmap]
rs9348868	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357127	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461714	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9469034	0.92[AMR][1000 genomes];0.92[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:56 , 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	chr6:11355200-11365200	Weak transcription	Left Ventricle	heart
3	chr6:11355200-11370800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:11357200-11371200	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr6:11357600-11365600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:11357600-11367600	Weak transcription	Aorta	Aorta
7	chr6:11357800-11364600	Weak transcription	HUVEC	blood vessel
8	chr6:11357800-11365200	Weak transcription	Lung	lung
9	chr6:11357800-11366600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:11357800-11370400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:11358000-11364400	Weak transcription	Spleen	Spleen
12	chr6:11358000-11367800	Weak transcription	Small Intestine	intestine
13	chr6:11358200-11367400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:11358800-11366400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:11358800-11367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:11359400-11369800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:11359600-11366400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:11360000-11366400	Weak transcription	Esophagus	oesophagus
19	chr6:11360200-11366800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:11360600-11364400	Weak transcription	Fetal Thymus	thymus
21	chr6:11360600-11364800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr6:11360800-11364400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:11360800-11364600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr6:11361000-11366400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:11361200-11364400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr6:11361200-11365800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:11361200-11366800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:11361200-11370600	Weak transcription	Thymus	Thymus
29	chr6:11361400-11364800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr6:11361400-11365000	Strong transcription	Primary B cells from cord blood	blood
31	chr6:11361600-11367200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:11362200-11365400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr6:11362400-11364600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:11362600-11366400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:11362800-11365600	Enhancers	HMEC	breast
36	chr6:11362800-11366800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr6:11363200-11365200	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr6:11363400-11364800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:11363600-11365200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:11363600-11365400	Strong transcription	Primary T cells from cord blood	blood
41	chr6:11363800-11367400	Enhancers	HepG2	liver
42	chr6:11364000-11364600	Genic enhancers	GM12878-XiMat	blood
43	chr6:11364000-11365200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:11364000-11365400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:11364200-11364400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:11364200-11364400	Enhancers	Pancreas	Pancrea
47	chr6:11364200-11364600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:11364200-11364600	Flanking Active TSS	NHEK	skin
49	chr6:11364200-11364800	Enhancers	Placenta	Placenta
50	chr6:11364200-11365400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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