Variant report

Variant	rs12645690
Chromosome Location	chr4:28550262-28550263
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:28535821..28537946-chr4:28547892..28550438,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10939223	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12645414	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645493	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646353	0.93[ASN][1000 genomes]
rs12648305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108631	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111564	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13125878	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13126238	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13135668	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13139196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13142519	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13151129	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1355895	0.93[ASN][1000 genomes]
rs1473899	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1514122	0.93[ASN][1000 genomes]
rs1514123	0.93[ASN][1000 genomes]
rs1514127	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16880756	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880758	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880781	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1972107	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972108	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988335	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2458604	0.93[ASN][1000 genomes]
rs2458605	0.93[ASN][1000 genomes]
rs2458609	0.90[ASN][1000 genomes]
rs2458610	0.90[ASN][1000 genomes]
rs2458611	0.90[ASN][1000 genomes]
rs2458615	0.86[ASN][1000 genomes]
rs2471697	0.92[ASN][1000 genomes]
rs2471713	0.93[ASN][1000 genomes]
rs2471714	0.93[ASN][1000 genomes]
rs2487818	0.86[ASN][1000 genomes]
rs292015	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs292016	0.88[ASN][1000 genomes]
rs292022	0.93[ASN][1000 genomes]
rs292023	0.93[ASN][1000 genomes]
rs2960595	0.92[ASN][1000 genomes]
rs2960596	0.93[ASN][1000 genomes]
rs2960598	0.93[ASN][1000 genomes]
rs34630635	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34879877	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35032764	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35166292	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35642022	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35769888	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4413395	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61793746	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66584086	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67828300	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664755	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7694223	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9790539	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs981579	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010133	chr4:28273244-28642942	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1014938	chr4:28277683-28642942	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2757926	chr4:28543958-28839437	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759239	chr4:28543958-28839437	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28539600-28555200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:28549600-28550800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:28549800-28550600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr4:28549800-28551000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr4:28550000-28551000	Active TSS	Right Atrium	heart
6	chr4:28550200-28550400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:28550200-28550600	Enhancers	Fetal Muscle Leg	muscle
8	chr4:28550200-28550800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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