Variant report

Variant	rs12529229
Chromosome Location	chr6:128915599-128915600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:128852805..128854332-chr6:128915251..128916981,2	MCF-7	breast:
2	chr6:128829914..128831519-chr6:128915307..128916935,2	MCF-7	breast:
3	chr6:128838418..128841487-chr6:128915011..128917718,3	MCF-7	breast:
4	chr6:128913529..128916197-chr6:128916953..128918922,3	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10085245	1.00[ASN][1000 genomes]
rs10085247	1.00[ASN][1000 genomes]
rs10085248	1.00[ASN][1000 genomes]
rs1012629	1.00[CHD][hapmap]
rs10223535	1.00[ASN][1000 genomes]
rs10872331	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11154439	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11154440	0.93[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751628	1.00[ASN][1000 genomes]
rs11752256	1.00[ASN][1000 genomes]
rs11753496	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756545	1.00[CHD][hapmap]
rs11758545	1.00[ASN][1000 genomes]
rs11758690	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11963575	1.00[ASN][1000 genomes]
rs12524679	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525214	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526634	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526667	1.00[ASN][1000 genomes]
rs12527086	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527265	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529511	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529947	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529948	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341584	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341585	1.00[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437323	1.00[ASN][1000 genomes]
rs1417896	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs1572964	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055952	1.00[ASN][1000 genomes]
rs17056043	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364020	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17364090	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17364118	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17364153	1.00[ASN][1000 genomes]
rs17460940	1.00[CHD][hapmap]
rs17461290	1.00[CHD][hapmap]
rs17461370	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17461759	1.00[ASN][1000 genomes]
rs1935131	1.00[ASN][1000 genomes]
rs2144376	0.93[CEU][hapmap]
rs2326702	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[ASN][1000 genomes]
rs55988836	1.00[ASN][1000 genomes]
rs57922933	1.00[ASN][1000 genomes]
rs62425737	1.00[ASN][1000 genomes]
rs62425738	1.00[ASN][1000 genomes]
rs62425739	1.00[ASN][1000 genomes]
rs62425740	1.00[ASN][1000 genomes]
rs62425742	1.00[ASN][1000 genomes]
rs62425743	1.00[ASN][1000 genomes]
rs62425744	1.00[ASN][1000 genomes]
rs62426790	1.00[ASN][1000 genomes]
rs62426791	1.00[ASN][1000 genomes]
rs62426792	1.00[ASN][1000 genomes]
rs62426793	1.00[ASN][1000 genomes]
rs62426794	1.00[ASN][1000 genomes]
rs62426795	1.00[ASN][1000 genomes]
rs62426796	1.00[ASN][1000 genomes]
rs62426797	1.00[ASN][1000 genomes]
rs62426798	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426799	1.00[ASN][1000 genomes]
rs62426800	1.00[ASN][1000 genomes]
rs62426801	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426804	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426805	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426806	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426840	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426841	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426842	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426844	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426845	0.88[EUR][1000 genomes]
rs62426846	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426847	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426848	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426849	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426851	1.00[ASN][1000 genomes]
rs62426853	1.00[ASN][1000 genomes]
rs62427780	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62427781	1.00[ASN][1000 genomes]
rs6569529	1.00[ASN][1000 genomes]
rs6569535	0.93[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs6569536	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6916294	0.87[EUR][1000 genomes]
rs714782	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356818	1.00[ASN][1000 genomes]
rs7356823	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs7356912	1.00[ASN][1000 genomes]
rs73591384	0.86[AFR][1000 genomes]
rs7454742	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766306	1.00[ASN][1000 genomes]
rs7738739	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739600	1.00[ASN][1000 genomes]
rs7748742	1.00[ASN][1000 genomes]
rs7751094	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751265	0.93[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7752487	1.00[ASN][1000 genomes]
rs7754729	0.90[EUR][1000 genomes]
rs7760287	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760572	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7760682	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765212	1.00[ASN][1000 genomes]
rs7768240	0.92[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7771701	1.00[ASN][1000 genomes]
rs9321122	1.00[ASN][1000 genomes]
rs9375578	0.93[CEU][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs9388647	0.90[EUR][1000 genomes]
rs9388648	0.87[EUR][1000 genomes]
rs9388649	0.90[EUR][1000 genomes]
rs9388650	0.90[EUR][1000 genomes]
rs9402055	0.90[EUR][1000 genomes]
rs9482892	1.00[ASN][1000 genomes]
rs9482893	1.00[ASN][1000 genomes]
rs9482897	1.00[ASN][1000 genomes]
rs9482902	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9482904	1.00[ASN][1000 genomes]
rs9491988	1.00[ASN][1000 genomes]
rs9492000	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492002	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492003	0.90[EUR][1000 genomes]
rs9492004	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492005	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492008	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492011	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492013	1.00[ASN][1000 genomes]
rs9492014	1.00[ASN][1000 genomes]
rs9492017	0.92[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492018	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492020	1.00[ASN][1000 genomes]
rs9492021	1.00[CHD][hapmap];1.00[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	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830801	chr6:128878436-129064667	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12529229	CHORDC1	trans	parietal	SCAN
rs12529229	RSPO3	cis	cerebellum	SCAN
rs12529229	C6orf174	cis	parietal	SCAN
rs12529229	SAMD3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128905400-128916000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:128915200-128919400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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