Variant report

Variant	rs12209878
Chromosome Location	chr6:11470141-11470142
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11468861..11470541-chr6:11472412..11474391,2	MCF-7	breast:
2	chr6:11469627..11471463-chr6:11472358..11475201,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10456073	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10456408	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10456409	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947294	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947297	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10947298	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10947330	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10947356	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947357	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947360	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10947400	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10947402	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10947403	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10947419	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12189605	0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12189776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12189829	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12190208	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12191269	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12191798	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12192607	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12192728	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12193222	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12193579	0.91[EUR][1000 genomes]
rs12194303	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12194423	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12194504	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12194522	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12194708	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12195075	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12195374	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12196157	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12197783	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12199737	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12201467	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12201652	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12202370	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12203104	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12203396	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12203843	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12207526	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12207574	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12208383	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12208387	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12209347	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209963	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12210023	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12210076	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12211376	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12211930	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12212790	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12214484	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12215719	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12524640	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12525082	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12526369	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16868542	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16868544	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16871460	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16871461	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16871481	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16871482	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs16871484	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17697296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17697372	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17697397	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17764876	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17764967	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2275398	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28651839	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs489364	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56132761	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6907207	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs9461842	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9461895	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9469217	0.91[JPT][hapmap]
rs9469363	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9469368	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9469544	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9469545	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9469546	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9469548	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9469550	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9469561	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9469563	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9791196	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11465800-11473200	Weak transcription	HepG2	liver
2	chr6:11466600-11470400	Enhancers	GM12878-XiMat	blood
3	chr6:11469200-11473000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:11469400-11470800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:11469800-11470200	Enhancers	Fetal Kidney	kidney

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