Variant report

Variant	rs4946273
Chromosome Location	chr6:117955898-117955899
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	chr6:117921339..117924676-chr6:117954310..117957194,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000047932	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10457315	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10457318	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10872153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153672	0.83[JPT][hapmap]
rs11961040	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12205963	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13211542	0.82[CHD][hapmap]
rs1501474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532680	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1827327	0.85[ASN][1000 genomes]
rs1967193	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967194	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071825	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2088870	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs210617	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs210630	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs210633	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs210637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs210639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs210642	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3752848	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4946265	0.87[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4946267	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4946269	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9285425	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs9285426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320612	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9320614	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9320616	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320617	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9374671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9374674	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9401014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9401019	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401023	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401025	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9489223	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9489238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9765895	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9767060	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];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	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
2	nsv521659	chr6:117950727-117955959	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv5449	chr6:117954646-117999751	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4946273	MCM9	cis	parietal	SCAN
rs4946273	BRD7P3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117950800-117975000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:117955400-117960000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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