Variant report

Variant	rs12192728
Chromosome Location	chr6:11490255-11490256
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	chr6:11489653..11491693-chr6:11494680..11496394,2	MCF-7	breast:
2	chr6:11438078..11439699-chr6:11488240..11490265,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10456073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10456408	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10456409	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10498678	0.81[ASN][1000 genomes]
rs10947294	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947297	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10947298	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10947299	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947300	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947301	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947305	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10947330	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10947360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10947400	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10947402	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947403	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12189605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12189776	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12189829	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12190208	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12191269	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12191798	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12192607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12193222	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12193579	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194303	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194423	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12194522	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12194708	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195075	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12195374	0.89[EUR][1000 genomes]
rs12196157	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12197783	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12199315	0.87[ASN][1000 genomes]
rs12199737	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12201467	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12201652	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12202370	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12203104	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12203396	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12203843	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12204093	0.84[ASN][1000 genomes]
rs12207526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12207574	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12208383	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12208387	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12209347	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12209878	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12209963	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12210023	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12210076	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12211376	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12211930	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12212790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12214484	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12215719	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12524640	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525082	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12526369	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16868542	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16868544	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16871460	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16871461	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16871481	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16871482	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs16871484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17697296	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17697372	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17697397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17764876	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17764967	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275398	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28651839	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56132761	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6907207	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs9461842	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9461895	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9469217	0.91[JPT][hapmap]
rs9469363	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9469368	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9469544	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9469545	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9469546	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9469548	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9469550	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9469561	0.89[EUR][1000 genomes]
rs9469563	0.89[EUR][1000 genomes]
rs9791196	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	esv3357042	chr6:11489266-11493964	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3372842	chr6:11489366-11493264	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3396914	chr6:11489566-11493564	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3441435	chr6:11489666-11493664	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 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	chr6:11480200-11491200	Weak transcription	Fetal Kidney	kidney
2	chr6:11483800-11495000	Weak transcription	Pancreas	Pancrea
3	chr6:11486800-11496000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:11486800-11496800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:11487000-11495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:11487400-11495800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:11487400-11495800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:11488000-11491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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