Variant report

Variant	rs2490247
Chromosome Location	chr6:80893192-80893193
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	chr6:80888084..80890010-chr6:80891656..80894939,3	K562	blood:
2	chr6:80873458..80875750-chr6:80890518..80893234,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10943700	1.00[EUR][1000 genomes]
rs151643	1.00[EUR][1000 genomes]
rs151659	1.00[EUR][1000 genomes]
rs16891543	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16891547	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16891556	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs187066	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs192130	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2182852	1.00[EUR][1000 genomes]
rs239499	1.00[EUR][1000 genomes]
rs239503	1.00[EUR][1000 genomes]
rs239557	1.00[CEU][hapmap]
rs239559	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs239561	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs239565	1.00[EUR][1000 genomes]
rs240215	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs240223	1.00[EUR][1000 genomes]
rs240227	1.00[EUR][1000 genomes]
rs2476827	0.82[AFR][1000 genomes]
rs2490225	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2490229	1.00[EUR][1000 genomes]
rs2490231	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2490233	1.00[EUR][1000 genomes]
rs2490237	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2490238	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs2490242	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2490246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2505931	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2505933	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2505934	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2505936	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2505938	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2505941	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2505943	1.00[EUR][1000 genomes]
rs2505947	1.00[EUR][1000 genomes]
rs2769338	1.00[EUR][1000 genomes]
rs2997392	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2997393	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56935289	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58231181	1.00[EUR][1000 genomes]
rs58621476	1.00[EUR][1000 genomes]
rs58678861	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60398437	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61477549	1.00[EUR][1000 genomes]
rs6454141	1.00[EUR][1000 genomes]
rs6912898	1.00[EUR][1000 genomes]
rs6925435	1.00[EUR][1000 genomes]
rs73748800	1.00[EUR][1000 genomes]
rs7748996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs806842	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9448918	1.00[EUR][1000 genomes]
rs9448921	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9448922	1.00[EUR][1000 genomes]
rs9448927	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	nsv830708	chr6:80844283-80996876	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv886309	chr6:80880138-80959885	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886310	chr6:80880138-81025879	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1033452	chr6:80888667-81000213	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80837000-80895200	Weak transcription	Fetal Intestine Small	intestine
2	chr6:80841200-80895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:80842200-80914200	Weak transcription	Primary B cells from cord blood	blood
4	chr6:80855200-80907000	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:80855200-80907200	Weak transcription	Ovary	ovary
6	chr6:80855400-80895400	Weak transcription	Fetal Stomach	stomach
7	chr6:80855800-80896000	Weak transcription	Aorta	Aorta
8	chr6:80863200-80907200	Weak transcription	Psoas Muscle	Psoas
9	chr6:80871400-80895800	Weak transcription	Right Ventricle	heart
10	chr6:80874000-80894000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:80874200-80899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:80875200-80893200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr6:80877600-80895800	Weak transcription	Esophagus	oesophagus
14	chr6:80878000-80921000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:80878600-80916000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:80878800-80907200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:80878800-80914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:80880600-80914200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr6:80882000-80896200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:80882400-80935400	Weak transcription	Dnd41	blood
21	chr6:80883800-80913200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:80885800-80919000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:80886000-80899000	Weak transcription	Liver	Liver
24	chr6:80889600-80893600	Enhancers	HUVEC	blood vessel
25	chr6:80889800-80895400	Weak transcription	Lung	lung
26	chr6:80891400-80907200	Weak transcription	Left Ventricle	heart
27	chr6:80891600-80895000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:80891600-80896000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:80891600-80898000	Weak transcription	Pancreas	Pancrea
30	chr6:80891600-80907400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:80891600-80931200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:80892200-80895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:80892200-80895400	Weak transcription	HMEC	breast
34	chr6:80892200-80913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:80892600-80895600	Weak transcription	NHEK	skin
36	chr6:80892800-80895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:80893000-80907400	Weak transcription	HSMM	muscle

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