Variant report

Variant	rs2449032
Chromosome Location	chr3:98720646-98720647
allele	C/T
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:95)

rs_ID	r²[population]
rs1383902	0.86[EUR][1000 genomes]
rs1383903	0.86[EUR][1000 genomes]
rs1383904	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1524228	0.81[AFR][1000 genomes]
rs1524229	0.81[AFR][1000 genomes]
rs1580376	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1585984	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1585985	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1585986	0.80[AFR][1000 genomes]
rs1905015	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1905016	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1905017	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1905018	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1905019	0.86[EUR][1000 genomes]
rs1905020	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1905021	0.85[EUR][1000 genomes]
rs2062060	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2062061	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2128048	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2128049	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2128050	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2262598	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2262599	0.86[EUR][1000 genomes]
rs2262600	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2262601	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2262602	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2262603	0.86[EUR][1000 genomes]
rs2449008	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2449009	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2449011	0.86[EUR][1000 genomes]
rs2449012	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449014	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449016	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449017	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449018	0.85[AMR][1000 genomes]
rs2449019	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449020	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449021	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449022	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449023	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449026	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449027	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449028	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449029	0.86[EUR][1000 genomes]
rs2449030	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449031	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449034	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449035	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449036	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2449038	0.85[EUR][1000 genomes]
rs2449059	0.82[AMR][1000 genomes]
rs2449065	0.81[AFR][1000 genomes]
rs2449067	0.81[AFR][1000 genomes]
rs2462219	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2462220	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2462221	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2462222	0.84[EUR][1000 genomes]
rs2462231	0.81[AFR][1000 genomes]
rs2462232	0.81[AFR][1000 genomes]
rs2462233	0.81[AFR][1000 genomes]
rs2462234	0.81[AFR][1000 genomes]
rs2462235	0.81[AFR][1000 genomes]
rs2462236	0.81[AFR][1000 genomes]
rs2462237	0.81[AFR][1000 genomes]
rs2470751	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470752	0.86[EUR][1000 genomes]
rs2470753	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470754	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2470755	0.82[AFR][1000 genomes]
rs2470756	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470758	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470769	0.86[EUR][1000 genomes]
rs2470776	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470785	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2470792	0.83[AMR][1000 genomes]
rs2470808	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2470815	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470816	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470818	0.86[EUR][1000 genomes]
rs2470819	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2470829	0.86[EUR][1000 genomes]
rs2470830	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470831	0.86[EUR][1000 genomes]
rs2470832	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2470833	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470836	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470840	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470842	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470843	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470844	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2470846	0.86[EUR][1000 genomes]
rs2470849	0.84[EUR][1000 genomes]
rs2929489	0.86[EUR][1000 genomes]
rs951093	0.81[AFR][1000 genomes]
rs9830705	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv980100	chr3:98714787-98766962	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2449032	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98711000-98721200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:98712800-98723000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:98713200-98721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:98717200-98730600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:98717600-98729200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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