Variant report

Variant	rs6794273
Chromosome Location	chr3:105177679-105177680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105166673..105169567-chr3:105177342..105179589,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11710166	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710857	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713535	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714275	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714277	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715283	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11716035	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11718405	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11718457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719817	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1898655	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955135	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2200473	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2399049	0.88[ASN][1000 genomes]
rs2895300	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34029528	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772542	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs3772544	0.88[ASN][1000 genomes]
rs3772547	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs481177	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs526297	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.88[ASN][1000 genomes]
rs57986655	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59322590	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598425	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs61522255	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771935	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6771987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786815	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73175407	0.88[ASN][1000 genomes]
rs73175433	0.88[ASN][1000 genomes]
rs73175435	0.88[ASN][1000 genomes]
rs73175442	0.88[ASN][1000 genomes]
rs73175449	0.88[ASN][1000 genomes]
rs73175451	0.88[ASN][1000 genomes]
rs73175463	0.88[ASN][1000 genomes]
rs73177459	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73177465	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73177470	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73177478	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73177489	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73177494	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73179378	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73179384	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181374	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181376	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181380	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181387	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181395	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181396	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181397	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73181401	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73183103	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73183108	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183112	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183114	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183115	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183185	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183186	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183187	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183188	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183198	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185106	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73185114	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73185115	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73189021	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73189028	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73189034	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73189060	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73192717	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73192730	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73192733	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73192737	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73192751	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73192754	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73192770	0.88[ASN][1000 genomes]
rs7647426	0.87[ASN][1000 genomes]
rs7647531	0.87[ASN][1000 genomes]
rs901280	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs978436	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105137400-105178600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:105144400-105185000	Weak transcription	Aorta	Aorta
3	chr3:105150800-105177800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:105167800-105185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:105168000-105177800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:105168000-105178600	Weak transcription	A549	lung
7	chr3:105168200-105179400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:105175200-105184800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:105175400-105179000	Weak transcription	Liver	Liver
10	chr3:105175400-105184400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:105175600-105178200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:105175600-105179000	Weak transcription	Brain Anterior Caudate	brain
13	chr3:105175800-105179000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:105176000-105177800	Weak transcription	Brain Angular Gyrus	brain
15	chr3:105177000-105177800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:105177000-105178000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:105177000-105179600	Enhancers	Osteobl	bone
18	chr3:105177200-105179200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:105177200-105179600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:105177400-105177800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:105177400-105178200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:105177400-105178400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:105177400-105179400	Enhancers	NH-A	brain
24	chr3:105177400-105180000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:105177400-105180200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr3:105177600-105177800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:105177600-105178800	Enhancers	NHEK	skin
28	chr3:105177600-105179000	Enhancers	HMEC	breast
29	chr3:105177600-105179000	Enhancers	HSMM	muscle
30	chr3:105177600-105179200	Enhancers	NHDF-Ad	bronchial
31	chr3:105177600-105179200	Enhancers	NHLF	lung
32	chr3:105177600-105180600	Enhancers	Brain Substantia Nigra	brain

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