Variant report

Variant	rs2085880
Chromosome Location	chr11:26392960-26392961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1037899	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs1037900	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs10767520	0.91[ASN][1000 genomes]
rs10767531	0.90[TSI][hapmap]
rs10834974	0.81[CHD][hapmap]
rs11029538	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11029543	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11029552	0.81[CHD][hapmap]
rs11500182	0.87[TSI][hapmap]
rs11824236	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12270746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12274334	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12274387	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12275964	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12283791	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12287530	1.00[CEU][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12287626	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12294597	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12294604	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13377552	0.92[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap]
rs1381177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381181	0.85[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1381183	0.84[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1461364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1461365	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1461366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1461368	0.90[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap]
rs1461371	0.90[TSI][hapmap]
rs1461373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1461374	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461376	0.85[ASN][1000 genomes]
rs1461377	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1461380	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1461382	0.94[ASW][hapmap];0.90[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1461384	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs1461385	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16915597	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1993745	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs2006942	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2045703	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2085878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2085879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126184	0.92[ASN][1000 genomes]
rs2126185	0.85[ASN][1000 genomes]
rs2169339	0.90[TSI][hapmap]
rs2199376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4444034	0.81[EUR][1000 genomes]
rs4923354	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs58872250	0.81[EUR][1000 genomes]
rs61877724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61877726	0.81[EUR][1000 genomes]
rs61877727	0.81[EUR][1000 genomes]
rs7104759	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7111512	0.83[TSI][hapmap]
rs7113405	0.81[CHD][hapmap]
rs7123997	0.90[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs7124839	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7128615	0.92[ASN][1000 genomes]
rs716700	0.81[EUR][1000 genomes]
rs716701	0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs719106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7480892	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7925675	0.94[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7928015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7931439	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7940514	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7942291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs7943164	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7945645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7946083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922246	0.90[TSI][hapmap]
rs961685	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9943473	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9943594	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422406	chr11:26329870-26473641	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription ZNF genes & repeats 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
rs2085880	SLC17A6	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:26392200-26393000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:26392600-26393800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:26392800-26393200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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