Variant report

Variant	rs560250
Chromosome Location	chr6:75795472-75795473
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	chr6:75794195..75796252-chr6:75800094..75801865,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs13437111	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16886197	1.00[CEU][hapmap]
rs16886390	1.00[CEU][hapmap]
rs16886391	1.00[CEU][hapmap]
rs16886411	1.00[CEU][hapmap]
rs171262	1.00[EUR][1000 genomes]
rs2300791	1.00[CEU][hapmap]
rs2300794	1.00[CEU][hapmap]
rs240372	1.00[EUR][1000 genomes]
rs240373	1.00[EUR][1000 genomes]
rs2883118	1.00[CEU][hapmap]
rs3822870	1.00[CEU][hapmap]
rs41266763	1.00[EUR][1000 genomes]
rs41269301	1.00[EUR][1000 genomes]
rs4388259	1.00[CEU][hapmap]
rs4449593	1.00[EUR][1000 genomes]
rs510507	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs545588	1.00[CEU][hapmap]
rs581649	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs60256732	1.00[EUR][1000 genomes]
rs61177673	1.00[EUR][1000 genomes]
rs658592	1.00[CEU][hapmap]
rs6927227	1.00[CEU][hapmap]
rs6931519	1.00[EUR][1000 genomes]
rs6932000	1.00[CEU][hapmap]
rs73462090	1.00[EUR][1000 genomes]
rs73747440	1.00[EUR][1000 genomes]
rs73747841	1.00[EUR][1000 genomes]
rs73747843	1.00[EUR][1000 genomes]
rs7738809	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7743883	1.00[CEU][hapmap]
rs7749000	1.00[CEU][hapmap]
rs7754400	1.00[CEU][hapmap]
rs7772503	1.00[CEU][hapmap]
rs7775765	1.00[CEU][hapmap]
rs7776027	1.00[CEU][hapmap]
rs9293988	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9443122	1.00[EUR][1000 genomes]
rs9443125	1.00[EUR][1000 genomes]
rs9447369	1.00[EUR][1000 genomes]
rs9447370	1.00[CEU][hapmap]
rs9447372	1.00[EUR][1000 genomes]
rs9447373	1.00[EUR][1000 genomes]
rs9447383	1.00[EUR][1000 genomes]
rs9447384	1.00[EUR][1000 genomes]
rs9447387	1.00[EUR][1000 genomes]
rs9447392	1.00[EUR][1000 genomes]
rs9447393	1.00[EUR][1000 genomes]
rs9447435	1.00[EUR][1000 genomes]
rs9447440	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022377	chr6:75762463-75919592	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv538309	chr6:75762463-75919592	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830697	chr6:75763095-75915029	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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 miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75789200-75800400	Strong transcription	Osteobl	bone
2	chr6:75789400-75800400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:75789800-75801000	Strong transcription	HSMM	muscle
4	chr6:75790000-75801200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:75792400-75797800	Weak transcription	Hela-S3	cervix
6	chr6:75793000-75804800	Strong transcription	HMEC	breast
7	chr6:75793200-75800800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:75793200-75802400	Strong transcription	NHLF	lung
9	chr6:75793200-75803400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:75793800-75801000	Strong transcription	NHDF-Ad	bronchial
11	chr6:75794000-75800000	Strong transcription	HSMMtube	muscle
12	chr6:75794200-75796200	Active TSS	Stomach Smooth Muscle	stomach
13	chr6:75794400-75795600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:75794400-75795600	Genic enhancers	Fetal Muscle Leg	muscle
15	chr6:75794400-75796200	Active TSS	Ovary	ovary
16	chr6:75794400-75800600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:75794600-75795600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr6:75794600-75795600	Bivalent Enhancer	Fetal Heart	heart
19	chr6:75794600-75795800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:75795000-75796600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:75795000-75797200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:75795000-75798800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:75795200-75795600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr6:75795200-75795600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
25	chr6:75795200-75795600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr6:75795200-75795600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
27	chr6:75795200-75795600	Enhancers	Liver	Liver
28	chr6:75795200-75795600	Enhancers	Brain Angular Gyrus	brain
29	chr6:75795200-75795600	Active TSS	Brain Substantia Nigra	brain
30	chr6:75795200-75795600	Genic enhancers	Fetal Stomach	stomach
31	chr6:75795200-75795600	Weak transcription	NH-A	brain
32	chr6:75795200-75795600	Enhancers	NHEK	skin
33	chr6:75795200-75796000	Genic enhancers	Adipose Nuclei	Adipose
34	chr6:75795200-75797200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:75795200-75798800	Weak transcription	Fetal Lung	lung
36	chr6:75795200-75799600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:75795200-75802600	Weak transcription	Esophagus	oesophagus
38	chr6:75795200-75803000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:75795200-75804800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:75795200-75804800	Weak transcription	Aorta	Aorta
41	chr6:75795200-75808000	Weak transcription	HUVEC	blood vessel
42	chr6:75795200-75811600	Weak transcription	Right Ventricle	heart
43	chr6:75795400-75795600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr6:75795400-75795600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:75795400-75795600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:75795400-75795600	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr6:75795400-75795600	Enhancers	Fetal Kidney	kidney
48	chr6:75795400-75795800	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr6:75795400-75797000	Weak transcription	Colon Smooth Muscle	Colon
50	chr6:75795400-75797800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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