Variant report

Variant	rs12193158
Chromosome Location	chr6:133506150-133506151
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:133151552..133152231-chr6:133505787..133506589,2	MCF-7	breast:
2	chr6:133505838..133506428-chr6:133832666..133833298,2	MCF-7	breast:
3	chr6:133505707..133506822-chr6:133833315..133834160,3	MCF-7	breast:
4	chr6:133505840..133506389-chr6:133833295..133833930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227954	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10872402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11154715	0.85[ASN][1000 genomes]
rs12154207	0.85[ASN][1000 genomes]
rs12190309	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12190728	0.85[ASN][1000 genomes]
rs12191026	0.85[ASN][1000 genomes]
rs12192839	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12193038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196069	0.85[ASN][1000 genomes]
rs12196492	0.85[ASN][1000 genomes]
rs12199555	0.85[ASN][1000 genomes]
rs12199738	0.84[ASN][1000 genomes]
rs12199958	0.85[ASN][1000 genomes]
rs12200393	0.85[ASN][1000 genomes]
rs12202540	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204996	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12206438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210216	0.85[ASN][1000 genomes]
rs12211999	0.85[ASN][1000 genomes]
rs12213690	0.85[ASN][1000 genomes]
rs1415858	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1856291	0.84[ASN][1000 genomes]
rs2180729	0.95[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28620929	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756869	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3756871	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3756872	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3777785	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs3777796	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3777799	0.86[CEU][hapmap]
rs55947866	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56377439	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59793266	0.85[ASN][1000 genomes]
rs62428596	0.85[ASN][1000 genomes]
rs62428597	0.85[ASN][1000 genomes]
rs62430275	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6569873	0.87[EUR][1000 genomes]
rs6912995	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6927143	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7746298	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7746390	0.85[ASN][1000 genomes]
rs7748926	0.85[ASN][1000 genomes]
rs7750376	0.85[CEU][hapmap]
rs7752905	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7754501	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7763647	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7766470	0.84[ASN][1000 genomes]
rs7767378	0.84[ASN][1000 genomes]
rs7767651	0.85[ASN][1000 genomes]
rs7773069	0.84[ASN][1000 genomes]
rs9321393	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9373038	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373041	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs9375940	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9375942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375943	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9375948	0.95[CEU][hapmap];0.80[CHB][hapmap];0.85[EUR][1000 genomes]
rs9375949	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9385640	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9385641	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9389052	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389059	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9389060	0.87[EUR][1000 genomes]
rs9389061	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs9399052	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399053	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399054	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9402484	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402485	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9402486	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9402487	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402489	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9402493	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9402494	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9402497	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs9483557	0.84[ASN][1000 genomes]
rs9483560	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493544	0.84[ASN][1000 genomes]
rs9493554	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428154	chr6:133271975-133522803	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2758080	chr6:133444719-133627364	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2759470	chr6:133444719-133627364	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv886677	chr6:133454738-133515602	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv524926	chr6:133492507-133510691	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv464058	chr6:133492507-133527935	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv604698	chr6:133492507-133527935	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv470862	chr6:133492507-133600402	Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133501200-133506400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:133505800-133507000	Enhancers	A549	lung
3	chr6:133506000-133506200	Enhancers	Fetal Lung	lung

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