Variant report

Variant	rs62406121
Chromosome Location	chr6:55909270-55909271
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: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1002249	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1002250	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1005783	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10456725	0.98[EUR][1000 genomes]
rs10948960	0.84[EUR][1000 genomes]
rs10948961	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10948964	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948965	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948966	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10948967	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10948968	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12190342	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12193200	0.81[EUR][1000 genomes]
rs12198766	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12201907	0.81[EUR][1000 genomes]
rs12204670	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12204682	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12205967	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12208960	0.81[EUR][1000 genomes]
rs12209568	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12211675	0.81[EUR][1000 genomes]
rs12212033	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12215085	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12216413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869623	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2143518	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3950156	0.95[EUR][1000 genomes]
rs60746236	0.81[EUR][1000 genomes]
rs62406117	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62406122	0.82[ASN][1000 genomes]
rs62406123	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs714069	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7739760	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7755390	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7773385	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9296819	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9296820	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9296821	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9296822	0.90[ASN][1000 genomes]
rs9370478	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9396169	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9464315	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9464327	0.95[EUR][1000 genomes]
rs9464334	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9475495	0.83[EUR][1000 genomes]
rs9475497	0.83[EUR][1000 genomes]
rs9475498	0.84[EUR][1000 genomes]
rs9475510	0.95[EUR][1000 genomes]
rs9475512	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9475513	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9475514	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9475515	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9475516	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9475517	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9475519	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9475530	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9475545	1.00[ASN][1000 genomes]
rs9475550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs980917	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	esv2584235	chr6:55831055-55910117	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	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
8	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
9	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
10	esv3529448	chr6:55902893-55910691	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3504061	chr6:55902893-55913891	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3529447	chr6:55903343-55910141	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	esv3529449	chr6:55903343-55910141	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	esv3504064	chr6:55903343-55913841	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv3504065	chr6:55903343-55913841	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv3474014	chr6:55907505-55918211	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv3474013	chr6:55907507-55918172	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3486610	chr6:55907534-55918254	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv3474015	chr6:55907553-55918186	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv3489357	chr6:55907556-55912831	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3489358	chr6:55907556-55912831	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv3474016	chr6:55907647-55918110	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv3486611	chr6:55907647-55918110	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
24	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	chr6:55908000-55909400	Enhancers	HSMM	muscle
5	chr6:55908200-55910400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:55908600-55910800	Weak transcription	Osteobl	bone
7	chr6:55909000-55910600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:55909200-55910600	Weak transcription	HUVEC	blood vessel
9	chr6:55909200-55910800	Weak transcription	Muscle Satellite Cultured Cells	--

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