Variant report

Variant	rs3805923
Chromosome Location	chr6:80887519-80887520
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80887382..80889174-chr6:80899148..80901683,2	MCF-7	breast:
2	chr6:80873495..80875635-chr6:80887027..80889000,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11961345	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs11961389	0.86[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11961412	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs11961506	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11961937	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11962441	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11963923	1.00[CEU][hapmap]
rs11967081	0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12110563	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324119	0.92[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs3749896	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805893	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs3805914	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805915	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805916	0.86[JPT][hapmap]
rs3805918	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812123	0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3812124	0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3812148	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3828750	0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59155686	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59460144	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59516180	0.85[ASN][1000 genomes]
rs66486409	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73477975	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs73477981	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73477985	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73479907	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73479909	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73479918	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73479932	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73479950	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479953	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479959	0.90[EUR][1000 genomes]
rs73479968	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73479980	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73482011	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73482029	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73482038	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs742834	0.84[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs806840	0.86[CHB][hapmap]
rs9343974	0.83[YRI][hapmap]

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	nsv524214	chr6:80853873-80892427	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80836400-80891200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:80837000-80895200	Weak transcription	Fetal Intestine Small	intestine
3	chr6:80839200-80889600	Weak transcription	Lung	lung
4	chr6:80841200-80895800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:80842200-80914200	Weak transcription	Primary B cells from cord blood	blood
6	chr6:80853800-80891800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:80855200-80907000	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:80855200-80907200	Weak transcription	Ovary	ovary
9	chr6:80855400-80895400	Weak transcription	Fetal Stomach	stomach
10	chr6:80855800-80896000	Weak transcription	Aorta	Aorta
11	chr6:80863200-80907200	Weak transcription	Psoas Muscle	Psoas
12	chr6:80868600-80891200	Weak transcription	Pancreas	Pancrea
13	chr6:80871400-80895800	Weak transcription	Right Ventricle	heart
14	chr6:80874000-80891000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:80874000-80894000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:80874200-80887600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:80874200-80888400	Weak transcription	Fetal Intestine Large	intestine
18	chr6:80874200-80899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:80875000-80891200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:80875200-80893200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:80875400-80891200	Weak transcription	Hela-S3	cervix
22	chr6:80875600-80891200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:80875800-80891200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:80877600-80895800	Weak transcription	Esophagus	oesophagus
25	chr6:80878000-80891200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:80878000-80921000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:80878600-80916000	Weak transcription	Adipose Nuclei	Adipose
28	chr6:80878800-80907200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:80878800-80914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:80880600-80891200	Weak transcription	Fetal Heart	heart
31	chr6:80880600-80914200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:80881800-80888600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr6:80882000-80891400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:80882000-80896200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:80882400-80887800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:80882400-80935400	Weak transcription	Dnd41	blood
37	chr6:80882600-80892200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:80883800-80913200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:80884800-80891200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:80885000-80891200	Weak transcription	NHLF	lung
41	chr6:80885200-80889600	Weak transcription	HUVEC	blood vessel
42	chr6:80885200-80891000	Weak transcription	HMEC	breast
43	chr6:80885400-80891800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:80885600-80889400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:80885600-80891200	Weak transcription	GM12878-XiMat	blood
46	chr6:80885800-80889400	Weak transcription	NHDF-Ad	bronchial
47	chr6:80885800-80889600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:80885800-80889600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:80885800-80891200	Weak transcription	HSMMtube	muscle
50	chr6:80885800-80919000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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