Variant report

Variant	rs6458545
Chromosome Location	chr6:12934302-12934303
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1014342	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12176425	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12526453	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1332844	0.92[CEU][hapmap]
rs1953088	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2210513	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2210514	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2210515	0.95[ASN][1000 genomes]
rs2210516	0.97[ASN][1000 genomes]
rs2327621	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2876303	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs34343839	0.83[EUR][1000 genomes]
rs4711863	0.84[CEU][hapmap]
rs4714951	0.81[CEU][hapmap]
rs4714955	0.90[CEU][hapmap]
rs4714990	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62386818	0.83[EUR][1000 genomes]
rs6912630	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6926919	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6940481	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs6941877	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7454157	0.92[CEU][hapmap]
rs7739181	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7750679	0.92[CEU][hapmap]
rs7751826	0.92[CEU][hapmap]
rs7760016	0.81[AMR][1000 genomes]
rs7760527	0.81[AMR][1000 genomes]
rs8180558	0.92[CEU][hapmap]
rs9296512	0.92[CEU][hapmap]
rs9296523	0.97[ASN][1000 genomes]
rs9296524	0.97[ASN][1000 genomes]
rs9296525	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296526	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296527	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9349390	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9357521	0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9357522	0.94[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9367262	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9369640	0.92[CEU][hapmap]
rs9369650	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9369652	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9369654	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9369655	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9369666	0.97[ASN][1000 genomes]
rs9381494	0.81[AMR][1000 genomes]
rs9381500	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9381507	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9381511	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9381512	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9381513	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9395214	0.92[CEU][hapmap]
rs9395226	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9395229	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9395231	0.97[ASN][1000 genomes]
rs9395237	0.97[ASN][1000 genomes]
rs9395240	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9463303	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs9472999	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv5202	chr6:12916229-12958517	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv817350	chr6:12922859-13137655	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12930400-12951800	Weak transcription	Fetal Brain Female	brain
2	chr6:12930800-12941600	Weak transcription	Brain Anterior Caudate	brain
3	chr6:12932400-12941400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:12933200-12944200	Weak transcription	Brain Germinal Matrix	brain

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