Variant report

Variant	rs17823609
Chromosome Location	chr14:63328525-63328526
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:63327519..63330186-chr14:63330862..63333796,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10047851	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10047852	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs10047856	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs10047884	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10047938	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs10130817	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10134277	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10134985	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10135128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10135421	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10135862	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs10136167	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs10138498	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10139105	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs10139268	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]
rs10139468	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs10140008	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10143260	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143966	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10146526	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10146673	1.00[CEU][hapmap]
rs10146879	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10147931	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap]
rs10148076	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10151264	0.94[ASN][1000 genomes]
rs10483757	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10483758	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs10483759	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10483760	0.92[CEU][hapmap]
rs10483762	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs10873163	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs10873164	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10873165	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12100661	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap]
rs12147279	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12586807	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap]
rs12587225	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs12587258	0.92[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12588293	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12588552	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12588586	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12589408	0.92[CEU][hapmap]
rs12881527	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1543437	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs17100446	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs17100497	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17223580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17223818	0.92[CEU][hapmap]
rs17223839	0.92[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs17223846	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs17823627	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17823807	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1950568	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1956018	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs1956026	0.92[CEU][hapmap]
rs2144775	0.95[ASN][1000 genomes]
rs2355741	0.85[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap]
rs243163	0.85[CEU][hapmap]
rs2860089	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap]
rs41419249	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs4146434	0.92[CEU][hapmap]
rs4146435	0.92[CEU][hapmap]
rs4270090	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs4899096	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4899100	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4902191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4902192	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap]
rs4902193	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs57087381	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59454582	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573462	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7146868	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs8004918	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs8005915	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs8007782	0.92[CEU][hapmap]
rs8013931	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8015097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8019236	0.89[CHB][hapmap]
rs9323421	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9323422	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs9888566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs9888605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]

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	nsv902015	chr14:63261862-63356253	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1042953	chr14:63314591-63384260	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv275351	chr14:63326784-63332083	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17823609	SIX1	cis	cerebellum	SCAN
rs17823609	C14orf39	cis	parietal	SCAN
rs17823609	SYT16	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:63328400-63328800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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