Variant report

Variant	rs1474588
Chromosome Location	chr6:15461709-15461710
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15456622..15459538-chr6:15460887..15465633,6	MCF-7	breast:
2	chr6:15244712..15246815-chr6:15459206..15462814,3	MCF-7	breast:
3	chr6:15454081..15456241-chr6:15460942..15462977,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271888	Chromatin interaction
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2076055	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2237117	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2237118	0.86[EUR][1000 genomes]
rs2237121	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2237124	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2237132	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237139	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2237141	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2237145	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2237150	0.81[CEU][hapmap]
rs2237156	0.84[CEU][hapmap]
rs2237157	0.81[CEU][hapmap]
rs2299045	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2299048	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2299053	0.82[CEU][hapmap]
rs2299054	0.84[CEU][hapmap]
rs3778652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4085876	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6459406	0.95[EUR][1000 genomes]
rs7754701	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7754755	0.94[EUR][1000 genomes]
rs9349979	0.86[EUR][1000 genomes]
rs9370813	0.82[CEU][hapmap]
rs9370817	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs9370819	0.85[EUR][1000 genomes]
rs9383051	0.80[CEU][hapmap]
rs9383054	0.84[CEU][hapmap]
rs9476827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15435800-15487600	Weak transcription	Colonic Mucosa	Colon
2	chr6:15440000-15468600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:15444600-15477400	Weak transcription	Hela-S3	cervix
4	chr6:15444800-15468800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:15445400-15474000	Weak transcription	NH-A	brain
6	chr6:15445600-15462600	Weak transcription	NHLF	lung
7	chr6:15446000-15462800	Weak transcription	HSMMtube	muscle
8	chr6:15446600-15479800	Weak transcription	Gastric	stomach
9	chr6:15448200-15479800	Weak transcription	Pancreas	Pancrea
10	chr6:15449800-15462800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:15452400-15475800	Weak transcription	Aorta	Aorta
12	chr6:15453000-15463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:15453000-15468600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:15453000-15481000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:15453600-15468800	Weak transcription	Dnd41	blood
16	chr6:15453800-15462600	Weak transcription	Osteobl	bone
17	chr6:15453800-15462800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:15454000-15462600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:15454200-15462600	Weak transcription	HSMM	muscle
20	chr6:15454200-15468800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:15454200-15468800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:15455200-15468800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr6:15455400-15462600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:15455400-15462800	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:15455400-15463000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:15455400-15463200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:15455400-15463600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:15455400-15468000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:15455400-15468600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:15455400-15468800	Weak transcription	Fetal Intestine Large	intestine
31	chr6:15455400-15468800	Weak transcription	HepG2	liver
32	chr6:15455400-15469600	Weak transcription	Fetal Intestine Small	intestine
33	chr6:15455400-15475600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:15455400-15475600	Weak transcription	Esophagus	oesophagus
35	chr6:15455600-15463000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:15455600-15468600	Weak transcription	K562	blood
37	chr6:15456400-15468600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:15456600-15462000	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:15456600-15467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:15457000-15462200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:15457000-15468800	Weak transcription	HMEC	breast
42	chr6:15457000-15480800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:15457200-15462600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:15457200-15462800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:15457400-15463800	Enhancers	Brain Hippocampus Middle	brain
46	chr6:15457600-15462000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr6:15457800-15462000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:15457800-15462200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr6:15458000-15462000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr6:15458400-15462800	Enhancers	H9 Cell Line	embryonic stem cell

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