Variant report

Variant	rs530066
Chromosome Location	chr6:117638124-117638125
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	chr6:117292832..117293821-chr6:117637901..117639050,5	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs17079053	0.91[EUR][1000 genomes]
rs17632578	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs1894674	0.82[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2243385	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs2243386	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs2301485	0.82[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2301486	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs3756891	0.82[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3798379	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473006	0.91[EUR][1000 genomes]
rs489576	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs492132	0.82[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs493451	1.00[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs493548	0.91[EUR][1000 genomes]
rs497186	0.82[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs498251	0.91[EUR][1000 genomes]
rs499199	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs499338	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs499599	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs501109	0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs506557	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs508278	1.00[CEU][hapmap];0.82[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs518987	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs528633	0.81[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs530713	0.91[EUR][1000 genomes]
rs541866	0.90[EUR][1000 genomes]
rs543230	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs543706	0.91[EUR][1000 genomes]
rs545537	0.91[EUR][1000 genomes]
rs546631	1.00[EUR][1000 genomes]
rs549557	0.84[EUR][1000 genomes]
rs552183	0.82[CEU][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes]
rs568514	0.91[EUR][1000 genomes]
rs573886	0.86[EUR][1000 genomes]
rs574664	0.91[EUR][1000 genomes]
rs575006	0.91[EUR][1000 genomes]
rs580099	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs581235	0.82[CEU][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs584647	1.00[EUR][1000 genomes]
rs592757	0.91[EUR][1000 genomes]
rs61077141	0.87[EUR][1000 genomes]
rs680920	0.87[EUR][1000 genomes]
rs687218	0.91[EUR][1000 genomes]
rs73566821	0.88[EUR][1000 genomes]
rs9481702	1.00[EUR][1000 genomes]
rs9489127	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9489135	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948766	chr6:117407275-117641016	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs530066	SLC35F1	cis	cerebellum	SCAN
rs530066	VGLL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117625800-117646600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:117628000-117643800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:117631400-117643400	Weak transcription	HSMMtube	muscle
4	chr6:117631400-117649200	Weak transcription	HSMM	muscle

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