Variant report

Variant	rs9475544
Chromosome Location	chr6:55910139-55910140
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	chr6:55904181..55905774-chr6:55908809..55911144,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs62406065	0.90[EUR][1000 genomes]
rs62406067	0.90[EUR][1000 genomes]
rs62406071	0.90[EUR][1000 genomes]
rs62406072	0.90[EUR][1000 genomes]
rs62406075	0.93[EUR][1000 genomes]
rs62406076	0.93[EUR][1000 genomes]
rs62406077	0.93[EUR][1000 genomes]
rs62406109	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406110	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406111	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406112	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406113	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406114	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406115	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406116	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406118	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406119	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406120	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406124	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406126	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7740526	0.90[EUR][1000 genomes]
rs7745793	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7749409	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7755079	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7756577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7775091	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464329	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464330	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464331	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464332	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9464335	0.90[EUR][1000 genomes]
rs9475520	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9475521	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9475522	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475523	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9475524	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475525	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475526	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475527	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475528	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475529	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475531	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475532	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475537	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475538	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475540	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475542	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475546	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9475551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv830665	chr6:55755560-55920219	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	esv3498415	chr6:55830704-55911231	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1023687	chr6:55868611-55940255	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv1020208	chr6:55870429-55932120	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv538227	chr6:55870429-55932120	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
9	esv3529448	chr6:55902893-55910691	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv3504061	chr6:55902893-55913891	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3529447	chr6:55903343-55910141	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3529449	chr6:55903343-55910141	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3504064	chr6:55903343-55913841	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3504065	chr6:55903343-55913841	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv3474014	chr6:55907505-55918211	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3474013	chr6:55907507-55918172	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv3486610	chr6:55907534-55918254	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3474015	chr6:55907553-55918186	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv3489357	chr6:55907556-55912831	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv3489358	chr6:55907556-55912831	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3474016	chr6:55907647-55918110	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv3486611	chr6:55907647-55918110	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv17318	chr6:55907704-55912800	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55899200-55920400	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:55905800-55911600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:55906200-55910800	Weak transcription	HSMMtube	muscle
4	chr6:55908200-55910400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:55908600-55910800	Weak transcription	Osteobl	bone
6	chr6:55909000-55910600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:55909200-55910600	Weak transcription	HUVEC	blood vessel
8	chr6:55909200-55910800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:55909400-55910800	Weak transcription	HSMM	muscle

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