Variant report

Variant	rs7039487
Chromosome Location	chr9:21709997-21709998
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	chr9:21709315..21710109-chr9:21789136..21789898,2	MCF-7	breast:

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10738597	0.80[ASN][1000 genomes]
rs10757236	0.86[ASN][1000 genomes]
rs10757238	0.81[ASN][1000 genomes]
rs10757239	0.81[ASN][1000 genomes]
rs10757240	0.81[ASN][1000 genomes]
rs10757241	0.81[ASN][1000 genomes]
rs10757242	0.81[ASN][1000 genomes]
rs10757245	0.80[ASN][1000 genomes]
rs10757246	0.80[ASN][1000 genomes]
rs10757247	0.80[ASN][1000 genomes]
rs10757251	0.80[ASN][1000 genomes]
rs10811584	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811592	0.86[ASN][1000 genomes]
rs10811595	0.86[ASN][1000 genomes]
rs10811600	0.81[ASN][1000 genomes]
rs10811601	0.81[ASN][1000 genomes]
rs10811602	0.81[ASN][1000 genomes]
rs10811604	0.81[ASN][1000 genomes]
rs10811605	0.81[ASN][1000 genomes]
rs12380505	0.88[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1335498	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335499	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335500	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335501	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1335502	0.81[ASN][1000 genomes]
rs1335505	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1335506	0.80[ASN][1000 genomes]
rs1335507	0.80[ASN][1000 genomes]
rs1335508	0.80[ASN][1000 genomes]
rs1345027	0.81[ASN][1000 genomes]
rs1372057	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1372058	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1372059	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1414232	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414234	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1414236	0.81[ASN][1000 genomes]
rs1414237	0.81[ASN][1000 genomes]
rs1414238	0.81[ASN][1000 genomes]
rs1414242	0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1414244	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs1414245	0.80[ASN][1000 genomes]
rs1414246	0.80[ASN][1000 genomes]
rs1414247	0.80[ASN][1000 genomes]
rs1414248	0.80[ASN][1000 genomes]
rs1414249	0.80[ASN][1000 genomes]
rs1452658	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1542075	0.84[CHB][hapmap]
rs1542076	0.84[CHB][hapmap]
rs17833407	0.83[CHB][hapmap]
rs1840050	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889680	0.92[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1965153	0.82[ASN][1000 genomes]
rs2004627	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2027162	0.81[ASN][1000 genomes]
rs2027163	0.81[ASN][1000 genomes]
rs2043991	0.85[ASN][1000 genomes]
rs2119466	0.80[ASN][1000 genomes]
rs2119467	0.80[ASN][1000 genomes]
rs2123338	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2165408	0.89[CHB][hapmap]
rs2165411	0.85[ASN][1000 genomes]
rs2383202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891159	0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2891160	0.81[ASN][1000 genomes]
rs2891164	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2891165	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35875883	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3928894	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs4350062	0.81[ASN][1000 genomes]
rs4352937	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4364717	0.89[CHB][hapmap]
rs4384075	0.80[ASN][1000 genomes]
rs4548267	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4560881	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4620363	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4636294	0.83[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs6475549	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475550	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475551	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6475552	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475554	0.86[ASN][1000 genomes]
rs6475555	0.86[ASN][1000 genomes]
rs6475564	0.85[ASN][1000 genomes]
rs6475566	0.81[ASN][1000 genomes]
rs6475568	0.81[ASN][1000 genomes]
rs6475569	0.81[ASN][1000 genomes]
rs6475574	0.80[ASN][1000 genomes]
rs6475585	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7021538	0.81[ASN][1000 genomes]
rs7023299	0.85[ASN][1000 genomes]
rs7023474	0.89[CHB][hapmap];0.80[JPT][hapmap]
rs7028913	0.86[ASN][1000 genomes]
rs7029040	0.86[ASN][1000 genomes]
rs7029166	0.86[ASN][1000 genomes]
rs7029274	0.86[ASN][1000 genomes]
rs7043827	0.85[ASN][1000 genomes]
rs7047136	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs751173	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7848524	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7852900	0.80[ASN][1000 genomes]
rs7853131	0.80[ASN][1000 genomes]
rs7854018	0.81[ASN][1000 genomes]
rs7854222	0.82[ASN][1000 genomes]
rs7855242	0.85[ASN][1000 genomes]
rs7857636	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858959	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7858991	0.81[ASN][1000 genomes]
rs7860576	0.86[ASN][1000 genomes]
rs7867994	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7868091	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7871345	0.85[ASN][1000 genomes]
rs7874319	0.81[ASN][1000 genomes]
rs869330	0.89[CHB][hapmap]
rs871024	0.89[CHB][hapmap]
rs9298821	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9298822	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9298823	0.84[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs9298824	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv471290	chr9:21694038-21721939	Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv892744	chr9:21694039-21746419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv1837210	chr9:21700795-21729895	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21707200-21712200	Enhancers	HMEC	breast
2	chr9:21707600-21710000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:21707600-21711000	Enhancers	NHEK	skin
4	chr9:21708400-21713000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:21708800-21710600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:21709200-21710600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:21709200-21710600	Weak transcription	NHDF-Ad	bronchial
8	chr9:21709200-21713000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:21709400-21710600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:21709400-21710800	Weak transcription	HSMM	muscle
11	chr9:21709400-21713400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:21709600-21710600	Weak transcription	Osteobl	bone
13	chr9:21709600-21710800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:21709600-21710800	Weak transcription	A549	lung
15	chr9:21709800-21710200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr9:21709800-21713000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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