Variant report

Variant	rs12899456
Chromosome Location	chr15:75364749-75364750
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	chr15:75362436..75364878-chr15:75367523..75369824,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12902887	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12905058	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12905176	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12905302	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12906126	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12906783	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12908596	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12908919	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12910578	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12911696	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16966775	0.81[AMR][1000 genomes]
rs16973563	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17336944	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1822324	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2304900	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34025186	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34073905	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34142677	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34183160	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34227381	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34268734	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34767908	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34820454	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34911644	0.95[AMR][1000 genomes]
rs35056361	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35205508	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35373072	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35375675	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35396991	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35406858	0.89[AMR][1000 genomes]
rs71401669	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs71401671	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs71401672	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71401673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71401675	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71401676	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71401677	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71434254	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7177045	0.81[AMR][1000 genomes]
rs8038911	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75342600-75364800	Weak transcription	Primary T cells from cord blood	blood
2	chr15:75356800-75366600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:75357000-75365400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr15:75358400-75368600	Weak transcription	Aorta	Aorta
5	chr15:75359200-75366200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr15:75360000-75370000	Weak transcription	Right Atrium	heart
7	chr15:75360600-75364800	Enhancers	Primary B cells from peripheral blood	blood
8	chr15:75360600-75366600	Enhancers	Primary B cells from cord blood	blood
9	chr15:75360800-75368200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:75361800-75365200	Weak transcription	Placenta	Placenta
11	chr15:75361800-75366800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr15:75362400-75365200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr15:75363000-75368400	Weak transcription	HepG2	liver
14	chr15:75363200-75365200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:75363600-75365600	Weak transcription	Fetal Thymus	thymus
16	chr15:75364200-75365800	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:75364200-75366000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:75364600-75366200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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