Variant report

Variant	rs62139487
Chromosome Location	chr2:40897573-40897574
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	chr2:40896962..40898911-chr2:40928950..40930770,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10048831	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10204982	0.89[EUR][1000 genomes]
rs10490260	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10490261	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10490265	0.83[EUR][1000 genomes]
rs1107932	0.90[EUR][1000 genomes]
rs11124759	0.84[EUR][1000 genomes]
rs1116005	0.85[AMR][1000 genomes]
rs12105490	0.89[EUR][1000 genomes]
rs12463684	0.83[EUR][1000 genomes]
rs12466428	0.90[EUR][1000 genomes]
rs12466571	0.88[EUR][1000 genomes]
rs12469284	0.90[EUR][1000 genomes]
rs12469295	0.90[EUR][1000 genomes]
rs12470937	0.84[EUR][1000 genomes]
rs12474457	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12474560	0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs12474649	0.96[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13414829	0.88[EUR][1000 genomes]
rs17026478	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026493	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17026498	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17039019	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17479653	0.82[EUR][1000 genomes]
rs1861302	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1861303	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2110791	0.87[EUR][1000 genomes]
rs2192816	0.88[EUR][1000 genomes]
rs2192819	0.89[EUR][1000 genomes]
rs2192820	0.90[EUR][1000 genomes]
rs28418485	0.84[EUR][1000 genomes]
rs28704849	0.84[EUR][1000 genomes]
rs34359856	0.97[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs3862989	0.88[EUR][1000 genomes]
rs4383382	0.80[EUR][1000 genomes]
rs4384832	0.87[EUR][1000 genomes]
rs4952640	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55670471	0.85[EUR][1000 genomes]
rs55690670	0.97[EUR][1000 genomes]
rs55772101	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs55814013	0.86[EUR][1000 genomes]
rs55878022	0.97[EUR][1000 genomes]
rs56121667	0.96[EUR][1000 genomes]
rs56321003	0.85[EUR][1000 genomes]
rs56336113	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs57243979	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57625048	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60819615	0.88[EUR][1000 genomes]
rs62139477	0.84[EUR][1000 genomes]
rs62139540	0.89[EUR][1000 genomes]
rs62139543	0.81[EUR][1000 genomes]
rs62139545	0.88[EUR][1000 genomes]
rs62139546	0.87[EUR][1000 genomes]
rs62141367	0.88[EUR][1000 genomes]
rs62141369	0.83[EUR][1000 genomes]
rs62141370	0.84[EUR][1000 genomes]
rs62141371	0.84[EUR][1000 genomes]
rs62141372	0.87[EUR][1000 genomes]
rs6708921	0.87[EUR][1000 genomes]
rs6712874	0.88[EUR][1000 genomes]
rs6720960	0.98[EUR][1000 genomes]
rs6721900	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733936	0.87[EUR][1000 genomes]
rs6734048	0.87[EUR][1000 genomes]
rs7563807	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7584710	0.97[EUR][1000 genomes]
rs767636	0.82[EUR][1000 genomes]
rs881189	0.89[EUR][1000 genomes]
rs888021	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv873917	chr2:40710953-41015998	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528865	chr2:40805427-41218810	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv873924	chr2:40835285-40926138	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv873925	chr2:40835285-40966719	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
6	nsv873926	chr2:40835285-40986860	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873927	chr2:40835285-41034225	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv470455	chr2:40835285-41059164	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv873928	chr2:40835285-41075134	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873929	chr2:40835285-41180690	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873931	chr2:40869165-40966719	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	nsv873932	chr2:40880043-40912597	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
13	nsv456441	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv581514	chr2:40882402-41064824	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv456452	chr2:40890416-40989061	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv581515	chr2:40890416-40989061	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr2:40896600-40899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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