Variant report

Variant	rs60239490
Chromosome Location	chr5:60306337-60306338
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60305681..60307942-chr5:60309957..60312620,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs16878535	1.00[AMR][1000 genomes]
rs16878537	1.00[AMR][1000 genomes]
rs16878539	1.00[AMR][1000 genomes]
rs16878544	1.00[AMR][1000 genomes]
rs3910825	1.00[AMR][1000 genomes]
rs4647074	1.00[AMR][1000 genomes]
rs4647116	1.00[AMR][1000 genomes]
rs55638584	1.00[AMR][1000 genomes]
rs55659107	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56020025	1.00[AMR][1000 genomes]
rs56043434	1.00[AMR][1000 genomes]
rs56071223	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56113732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56256328	1.00[AMR][1000 genomes]
rs56287212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56306823	1.00[AMR][1000 genomes]
rs56320246	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56386934	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57108975	1.00[AMR][1000 genomes]
rs57251027	1.00[AMR][1000 genomes]
rs57366470	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58930565	1.00[AMR][1000 genomes]
rs59453232	1.00[AMR][1000 genomes]
rs6449516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6860439	1.00[AMR][1000 genomes]
rs6869855	1.00[AMR][1000 genomes]
rs6870631	1.00[AMR][1000 genomes]
rs6881713	1.00[AMR][1000 genomes]
rs6881960	1.00[AMR][1000 genomes]
rs6885974	1.00[AMR][1000 genomes]
rs73759415	1.00[AMR][1000 genomes]
rs73759422	1.00[AMR][1000 genomes]
rs73759426	1.00[AMR][1000 genomes]
rs73759427	1.00[AMR][1000 genomes]
rs73759430	1.00[AMR][1000 genomes]
rs73759431	1.00[AMR][1000 genomes]
rs73759432	1.00[AMR][1000 genomes]
rs73759434	1.00[AMR][1000 genomes]
rs73759435	1.00[AMR][1000 genomes]
rs73759437	1.00[AMR][1000 genomes]
rs73759441	1.00[AMR][1000 genomes]
rs73759445	1.00[AMR][1000 genomes]
rs73759446	1.00[AMR][1000 genomes]
rs73759447	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759450	1.00[AMR][1000 genomes]
rs73759452	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759458	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759459	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759461	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73759468	1.00[AMR][1000 genomes]
rs73759469	1.00[AMR][1000 genomes]
rs73759470	1.00[AMR][1000 genomes]
rs73759471	1.00[AMR][1000 genomes]
rs73759475	1.00[AMR][1000 genomes]
rs7701710	0.81[AFR][1000 genomes]
rs7701959	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7717284	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer 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
2	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv598305	chr5:60116613-60308836	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv881714	chr5:60116613-60313015	Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv598307	chr5:60129361-60308836	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv881716	chr5:60129361-60313015	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv462199	chr5:60129361-60329624	Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv598308	chr5:60129361-60329624	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv598310	chr5:60135985-60308836	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv598311	chr5:60136626-60308836	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv520871	chr5:60141245-60320157	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	nsv598312	chr5:60147754-60313015	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv881718	chr5:60147754-60313015	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	nsv933573	chr5:60224875-60309751	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv881721	chr5:60232646-60344399	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	nsv933769	chr5:60240706-60309751	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv518695	chr5:60266875-60329624	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60266200-60317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:60302200-60311400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links