Variant report

Variant	rs1332841
Chromosome Location	chr6:12875054-12875055
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	chr6:12869699..12871951-chr6:12874630..12877257,2	MCF-7	breast:
2	chr6:12863378..12865957-chr6:12874022..12876094,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10948235	1.00[CHB][hapmap]
rs10948244	1.00[CHB][hapmap]
rs10948247	1.00[CHB][hapmap]
rs12523719	1.00[CHB][hapmap]
rs12526453	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12528956	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap]
rs12530250	1.00[JPT][hapmap]
rs13201878	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13217579	1.00[CHB][hapmap]
rs13219256	1.00[CHD][hapmap]
rs1332840	1.00[CHB][hapmap]
rs1332845	1.00[CHD][hapmap]
rs1332847	1.00[CHD][hapmap]
rs1360579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412740	1.00[CHB][hapmap]
rs1412741	1.00[CHB][hapmap]
rs1412744	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1412751	1.00[CHB][hapmap]
rs1412752	1.00[CHB][hapmap]
rs1412753	1.00[CHB][hapmap]
rs1537340	1.00[CHD][hapmap]
rs1572000	1.00[CHB][hapmap]
rs1572002	1.00[CHB][hapmap]
rs17617207	1.00[CHB][hapmap]
rs17679417	1.00[CHB][hapmap]
rs17679501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1953089	1.00[CHB][hapmap]
rs2327619	1.00[CHB][hapmap]
rs2327621	1.00[CHD][hapmap]
rs4131857	1.00[JPT][hapmap]
rs4331981	1.00[JPT][hapmap]
rs4711857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714866	1.00[CHB][hapmap]
rs4714870	1.00[CHB][hapmap]
rs4714946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458461	1.00[CHB][hapmap]
rs6458503	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs66867947	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909834	1.00[CHB][hapmap]
rs6916334	1.00[CHB][hapmap]
rs6917493	1.00[CHB][hapmap]
rs6924150	1.00[CHB][hapmap]
rs6938417	1.00[CHB][hapmap]
rs6941422	1.00[CHB][hapmap]
rs6941624	1.00[CHB][hapmap]
rs7739181	1.00[JPT][hapmap]
rs7748950	1.00[CHB][hapmap]
rs7757205	1.00[CHB][hapmap]
rs7757858	1.00[CHB][hapmap]
rs7760140	1.00[CHB][hapmap]
rs7760286	1.00[CHB][hapmap]
rs7770745	1.00[CHB][hapmap]
rs7771962	1.00[CHB][hapmap]
rs7775901	1.00[JPT][hapmap]
rs7776079	1.00[CHB][hapmap]
rs883947	1.00[CHB][hapmap]
rs9296464	1.00[CHB][hapmap]
rs9296494	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9395190	1.00[CHB][hapmap]
rs944766	1.00[CHB][hapmap]
rs944767	1.00[CHB][hapmap]
rs9463106	1.00[CHB][hapmap]
rs9463110	1.00[CHB][hapmap]
rs9463134	1.00[CHB][hapmap]
rs9472551	1.00[CHB][hapmap]
rs9472777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9473086	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs950720	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1027534	chr6:12858048-12877597	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1332841	PAK1IP1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12867400-12887600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:12867600-12886800	Weak transcription	Brain Anterior Caudate	brain
3	chr6:12867800-12876800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:12870400-12885200	Weak transcription	Brain Germinal Matrix	brain
5	chr6:12871600-12876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:12871600-12876800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:12873600-12875200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:12873800-12875800	Enhancers	NH-A	brain
9	chr6:12873800-12875800	Enhancers	NHDF-Ad	bronchial
10	chr6:12873800-12876200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:12874200-12876800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:12874800-12875400	Enhancers	Fetal Brain Female	brain

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