Variant report

Variant	rs9489530
Chromosome Location	chr6:119118427-119118428
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	chr6:119091223..119093581-chr6:119115948..119118630,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10080855	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1087453	0.82[AMR][1000 genomes]
rs1087454	0.86[AMR][1000 genomes]
rs11153785	0.82[AMR][1000 genomes]
rs12191819	0.86[EUR][1000 genomes]
rs12194515	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12196440	0.86[EUR][1000 genomes]
rs12197931	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12200499	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12203353	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12203542	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12207299	0.84[ASN][1000 genomes]
rs12210027	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12212179	0.86[EUR][1000 genomes]
rs12214434	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12216519	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1321836	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1407205	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1407206	0.86[EUR][1000 genomes]
rs284914	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs284915	0.83[AMR][1000 genomes]
rs284918	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs284920	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs376225	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3798594	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3798595	0.86[EUR][1000 genomes]
rs3798599	0.86[EUR][1000 genomes]
rs388987	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41292550	0.86[EUR][1000 genomes]
rs41292554	0.86[EUR][1000 genomes]
rs56895036	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs706971	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72966811	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72966851	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72966873	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72966896	0.86[EUR][1000 genomes]
rs72970448	0.86[AMR][1000 genomes]
rs768995	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs768996	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs794611	0.86[AMR][1000 genomes]
rs797017	0.86[AMR][1000 genomes]
rs9481862	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9481867	0.86[EUR][1000 genomes]
rs9481868	0.86[EUR][1000 genomes]
rs9481869	0.86[EUR][1000 genomes]
rs9481870	0.86[EUR][1000 genomes]
rs9481871	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9481872	0.86[EUR][1000 genomes]
rs9481878	0.82[AMR][1000 genomes]
rs9489531	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9489535	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489536	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489539	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489540	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489543	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489544	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9489547	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv886568	chr6:119044453-119132164	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv886569	chr6:119055873-119132164	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119108800-119136000	Weak transcription	Aorta	Aorta
2	chr6:119109200-119121600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:119109400-119121400	Weak transcription	Primary T cells from cord blood	blood
4	chr6:119109800-119121200	Weak transcription	Left Ventricle	heart
5	chr6:119110200-119121600	Weak transcription	Thymus	Thymus
6	chr6:119113800-119136000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:119116000-119119000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:119116600-119136200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:119117200-119119400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:119117400-119121200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:119117600-119121200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:119117800-119119000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:119117800-119121200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:119117800-119121200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:119117800-119121200	Weak transcription	HepG2	liver
16	chr6:119117800-119125800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:119118000-119121200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:119118000-119121400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:119118200-119118600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:119118200-119118600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:119118200-119121200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:119118200-119121200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr6:119118400-119119000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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