Variant report

Variant	rs6879499
Chromosome Location	chr5:28913517-28913518
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	chr5:28910494..28912517-chr5:28913196..28915967,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10036651	0.90[EUR][1000 genomes]
rs10037546	0.97[EUR][1000 genomes]
rs10040428	0.94[EUR][1000 genomes]
rs10078393	0.97[EUR][1000 genomes]
rs1019768	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11738914	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11744174	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12189440	0.89[EUR][1000 genomes]
rs12654800	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13156975	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13166267	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13167204	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13167436	0.90[EUR][1000 genomes]
rs13169800	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13172660	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13172713	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13172749	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13175378	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13188965	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13189228	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13189582	0.93[EUR][1000 genomes]
rs1423286	0.81[ASN][1000 genomes]
rs1864781	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2014071	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2033222	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2033223	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2195363	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548010	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2548013	0.81[AMR][1000 genomes]
rs2548014	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2554911	0.95[EUR][1000 genomes]
rs2554913	0.92[EUR][1000 genomes]
rs395785	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4050944	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs411622	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs434405	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs451888	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs453464	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs458670	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs458774	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs460138	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs463248	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs463572	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs465704	0.81[EUR][1000 genomes]
rs466209	0.81[EUR][1000 genomes]
rs467107	0.81[EUR][1000 genomes]
rs467378	0.80[EUR][1000 genomes]
rs486473	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs573961	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs629546	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs629925	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6450663	0.92[EUR][1000 genomes]
rs646799	0.83[EUR][1000 genomes]
rs654983	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs655444	0.84[EUR][1000 genomes]
rs6869025	0.91[EUR][1000 genomes]
rs694504	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs825319	0.96[EUR][1000 genomes]
rs94374	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs94375	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs94376	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026700	chr5:28067287-28978638	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv537707	chr5:28067287-28978638	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1029219	chr5:28370908-29086506	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv537710	chr5:28370908-29086506	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv880822	chr5:28498983-28959648	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv462027	chr5:28707892-28986950	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv597712	chr5:28707892-28986950	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv881229	chr5:28739011-28921260	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv880313	chr5:28779357-28915911	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv880470	chr5:28786844-28921260	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv880374	chr5:28786844-28955799	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv881575	chr5:28786844-28979728	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv881649	chr5:28786844-29007308	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv881344	chr5:28786844-29017460	Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv880855	chr5:28786844-29129027	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv471008	chr5:28806256-28915911	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv881250	chr5:28806256-28915911	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv881525	chr5:28806256-28921260	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	nsv462048	chr5:28806256-28970173	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv462049	chr5:28806256-28970173	Enhancers Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv597730	chr5:28806256-28970173	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv462051	chr5:28806256-28977674	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv597731	chr5:28806256-28977674	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
24	nsv462052	chr5:28806256-28986950	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
25	nsv462053	chr5:28806256-28986950	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
26	nsv462054	chr5:28806256-28986950	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	nsv597732	chr5:28806256-28986950	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
28	nsv881674	chr5:28806256-29007308	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
29	nsv880318	chr5:28806256-29017460	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
30	nsv880410	chr5:28806256-29017460	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
31	nsv462072	chr5:28811789-28986950	Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
32	nsv462074	chr5:28811789-28986950	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
33	nsv597739	chr5:28811789-28986950	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
34	nsv881224	chr5:28815962-28927036	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
35	nsv830243	chr5:28884069-29062804	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:28913400-28914800	Enhancers	HUES48 Cell Line	embryonic stem cell

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