Variant report

Variant	rs1322399
Chromosome Location	chr6:86070352-86070353
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	chr6:86068019..86071136-chr6:86192476..86194796,3	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1026064	0.88[ASN][1000 genomes]
rs1028637	0.89[ASN][1000 genomes]
rs10498953	0.93[ASN][1000 genomes]
rs10498954	0.93[ASN][1000 genomes]
rs11758883	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322400	0.89[ASN][1000 genomes]
rs1322407	0.92[ASN][1000 genomes]
rs1322408	0.92[ASN][1000 genomes]
rs1322409	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1322410	0.91[ASN][1000 genomes]
rs1407446	0.89[ASN][1000 genomes]
rs1575309	0.89[ASN][1000 genomes]
rs17216936	0.89[ASN][1000 genomes]
rs17216964	0.89[ASN][1000 genomes]
rs17217290	0.89[ASN][1000 genomes]
rs17217313	0.91[ASN][1000 genomes]
rs17217341	0.91[ASN][1000 genomes]
rs17816793	0.89[ASN][1000 genomes]
rs1853254	0.89[ASN][1000 genomes]
rs2181188	0.89[ASN][1000 genomes]
rs2208726	0.90[ASN][1000 genomes]
rs2208727	0.89[ASN][1000 genomes]
rs2224595	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2324775	0.93[ASN][1000 genomes]
rs4337908	0.92[ASN][1000 genomes]
rs4706233	0.91[ASN][1000 genomes]
rs4707192	0.89[ASN][1000 genomes]
rs4707193	0.89[ASN][1000 genomes]
rs4707194	0.85[AMR][1000 genomes]
rs4707196	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707197	0.84[ASN][1000 genomes]
rs5019880	0.89[ASN][1000 genomes]
rs5019881	0.89[ASN][1000 genomes]
rs5019882	0.89[ASN][1000 genomes]
rs5019883	0.89[ASN][1000 genomes]
rs5019884	0.89[ASN][1000 genomes]
rs56679761	0.86[ASN][1000 genomes]
rs57115758	0.89[ASN][1000 genomes]
rs57214768	0.91[ASN][1000 genomes]
rs57393053	0.91[ASN][1000 genomes]
rs57464713	0.84[ASN][1000 genomes]
rs57915056	0.89[ASN][1000 genomes]
rs58387111	0.99[ASN][1000 genomes]
rs58873354	0.89[ASN][1000 genomes]
rs59797978	0.91[ASN][1000 genomes]
rs59825200	0.84[ASN][1000 genomes]
rs60034184	0.89[ASN][1000 genomes]
rs60308797	0.89[ASN][1000 genomes]
rs60696184	0.84[ASN][1000 genomes]
rs60968245	0.87[ASN][1000 genomes]
rs61200746	0.87[ASN][1000 genomes]
rs61536412	0.93[ASN][1000 genomes]
rs61620438	0.84[ASN][1000 genomes]
rs62420143	0.89[ASN][1000 genomes]
rs62420144	0.89[ASN][1000 genomes]
rs62420145	0.89[ASN][1000 genomes]
rs62444622	0.93[ASN][1000 genomes]
rs62444623	0.93[ASN][1000 genomes]
rs62444624	0.93[ASN][1000 genomes]
rs62444625	0.92[ASN][1000 genomes]
rs62444626	0.93[ASN][1000 genomes]
rs62444627	0.93[ASN][1000 genomes]
rs62444629	0.93[ASN][1000 genomes]
rs62444632	1.00[ASN][1000 genomes]
rs6908264	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6930866	0.92[ASN][1000 genomes]
rs6938795	0.89[ASN][1000 genomes]
rs6942223	0.84[ASN][1000 genomes]
rs7740378	0.91[ASN][1000 genomes]
rs7744735	0.91[ASN][1000 genomes]
rs7745109	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9450243	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450248	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs950030	0.88[ASN][1000 genomes]
rs9689843	0.83[ASN][1000 genomes]
rs969918	0.87[ASN][1000 genomes]
rs970568	0.89[ASN][1000 genomes]
rs970569	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv830721	chr6:85987644-86147414	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1019960	chr6:86023236-86136666	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86058200-86070400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:86058600-86071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:86067000-86070400	Weak transcription	HUVEC	blood vessel
4	chr6:86067400-86071000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:86067600-86071800	Enhancers	A549	lung
6	chr6:86067600-86074400	Enhancers	NHDF-Ad	bronchial
7	chr6:86067800-86074400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:86069000-86070400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:86069000-86071200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:86069000-86074400	Enhancers	NHLF	lung
11	chr6:86069200-86072800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:86069200-86073200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:86069200-86073200	Enhancers	HMEC	breast
14	chr6:86069200-86074200	Enhancers	Osteobl	bone
15	chr6:86069200-86074400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:86069400-86071600	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr6:86069400-86073000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr6:86069400-86073200	Enhancers	Hela-S3	cervix
19	chr6:86069400-86073200	Enhancers	NHEK	skin
20	chr6:86069600-86071600	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:86069600-86071800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr6:86069600-86073200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:86069800-86071200	Enhancers	HepG2	liver
24	chr6:86069800-86071800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:86069800-86071800	Enhancers	HSMM	muscle
26	chr6:86070000-86072600	Enhancers	Placenta	Placenta
27	chr6:86070200-86070600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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