Variant report

Variant	rs11211471
Chromosome Location	chr1:47618714-47618715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10789500	0.85[EUR][1000 genomes]
rs10789501	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10789503	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890446	0.82[MEX][hapmap]
rs10890457	0.87[CEU][hapmap];0.88[TSI][hapmap]
rs10890460	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10890462	0.82[EUR][1000 genomes]
rs10890464	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs10890465	0.83[EUR][1000 genomes]
rs10890466	0.84[EUR][1000 genomes]
rs10890467	0.84[EUR][1000 genomes]
rs10890468	0.85[EUR][1000 genomes]
rs10890470	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1110425	0.82[EUR][1000 genomes]
rs11211446	0.87[CEU][hapmap]
rs11211450	0.83[EUR][1000 genomes]
rs11211451	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs11211454	0.81[EUR][1000 genomes]
rs11211457	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11211459	0.82[EUR][1000 genomes]
rs11211463	0.82[EUR][1000 genomes]
rs11211464	0.88[EUR][1000 genomes]
rs11211472	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211475	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12037014	0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs12042073	0.84[EUR][1000 genomes]
rs12046348	0.84[EUR][1000 genomes]
rs12046525	0.84[EUR][1000 genomes]
rs12124648	0.84[EUR][1000 genomes]
rs12734327	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1847222	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs1847223	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1847224	0.83[EUR][1000 genomes]
rs1967756	0.83[EUR][1000 genomes]
rs1967757	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs2016160	0.87[CEU][hapmap]
rs2208772	0.85[EUR][1000 genomes]
rs2224622	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2494248	0.92[CEU][hapmap];0.93[GIH][hapmap]
rs2742079	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2798352	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2798356	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2821082	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28462300	0.84[EUR][1000 genomes]
rs28796303	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3850876	0.84[EUR][1000 genomes]
rs4314923	0.82[EUR][1000 genomes]
rs4926785	0.87[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs4926786	0.82[EUR][1000 genomes]
rs4926787	0.82[EUR][1000 genomes]
rs4926788	0.82[EUR][1000 genomes]
rs4926789	0.82[EUR][1000 genomes]
rs4926791	0.82[EUR][1000 genomes]
rs4926792	0.82[EUR][1000 genomes]
rs4926793	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs4926797	0.82[EUR][1000 genomes]
rs4926804	0.82[EUR][1000 genomes]
rs4926805	0.81[EUR][1000 genomes]
rs4926809	0.82[EUR][1000 genomes]
rs4926826	0.83[EUR][1000 genomes]
rs4926869	0.83[EUR][1000 genomes]
rs4926918	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6588388	0.81[EUR][1000 genomes]
rs6588389	0.80[EUR][1000 genomes]
rs6664392	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs6664496	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs6675902	0.82[EUR][1000 genomes]
rs6690005	0.87[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6693145	0.82[EUR][1000 genomes]
rs6701611	0.82[EUR][1000 genomes]
rs7512729	0.81[EUR][1000 genomes]
rs7519903	0.82[EUR][1000 genomes]
rs7522639	0.83[EUR][1000 genomes]
rs7526674	0.83[EUR][1000 genomes]
rs7540264	0.82[EUR][1000 genomes]
rs7545034	1.00[CHD][hapmap]
rs7545399	0.83[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs7547893	0.81[EUR][1000 genomes]
rs760440	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs760441	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs760442	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs911903	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs911909	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9633421	0.84[EUR][1000 genomes]
rs9793471	0.83[MEX][hapmap];0.86[TSI][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	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv870705	chr1:47533705-47620126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871010	chr1:47533705-47637999	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv870899	chr1:47548974-47637999	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11211471	SPATA6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47596400-47641000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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