Variant report

Variant	rs35006699
Chromosome Location	chr3:98652616-98652617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10428160	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10589669	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11552978	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12107272	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12108018	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12108142	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13059624	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13065136	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13068317	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072410	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13074614	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13074787	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13076960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078549	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13079960	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13080057	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13081992	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13083238	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13083613	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13083934	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13084692	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13087627	0.98[EUR][1000 genomes]
rs13087631	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13088532	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13091170	0.98[EUR][1000 genomes]
rs13091236	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13091956	0.82[EUR][1000 genomes]
rs13093128	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13096085	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13097876	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13100915	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13100937	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1983009	0.84[EUR][1000 genomes]
rs2439232	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs2454687	0.89[EUR][1000 genomes]
rs34008360	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34269725	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34279227	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34284740	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34394867	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34428696	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34470469	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34479374	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34489202	0.98[EUR][1000 genomes]
rs34688367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34711372	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34725039	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34826460	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34848749	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860591	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35025156	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35076733	0.93[EUR][1000 genomes]
rs35098355	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35103318	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35219252	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35234681	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35239055	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35312318	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35366262	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35422064	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35499232	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35514544	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35526367	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35539438	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35592768	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35764973	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35854439	0.82[EUR][1000 genomes]
rs35914268	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35947493	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35947806	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36032715	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36098932	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36157152	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36160001	0.84[EUR][1000 genomes]
rs36175276	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41267851	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55644421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56083233	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56094988	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56246599	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56408882	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6764579	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6805362	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71124004	0.83[EUR][1000 genomes]
rs71311393	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71311394	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71311397	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71311398	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71311402	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71313504	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313506	0.91[EUR][1000 genomes]
rs71313508	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313509	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313510	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313511	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7614053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35006699	ST3GAL6	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98643000-98663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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