Variant report

Variant	rs6440280
Chromosome Location	chr3:98706331-98706332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 229 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:224)

rs_ID	r²[population]
rs1123293	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054181	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383902	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1383903	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1383904	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1383905	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383910	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481634	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481635	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481636	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481637	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524227	0.82[AMR][1000 genomes]
rs1524228	0.82[AMR][1000 genomes]
rs1524229	0.82[AMR][1000 genomes]
rs1580372	0.82[AMR][1000 genomes]
rs1580374	0.83[AMR][1000 genomes]
rs1580375	0.81[AMR][1000 genomes]
rs1580376	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1585984	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1585985	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1585986	0.82[AMR][1000 genomes]
rs1585988	0.81[AMR][1000 genomes]
rs1837500	0.86[ASN][1000 genomes]
rs1875086	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1905015	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1905016	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1905017	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1905018	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1905019	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1905020	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1905021	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1967009	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028393	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062059	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062060	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2062061	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2119187	0.82[ASN][1000 genomes]
rs2119188	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2128048	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2128049	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2128050	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2128051	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2128054	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246861	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249740	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2262597	0.81[AMR][1000 genomes]
rs2262598	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2262599	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2262600	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2262602	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2262603	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2439213	0.81[AMR][1000 genomes]
rs2439218	0.81[AMR][1000 genomes]
rs2439220	0.82[ASN][1000 genomes]
rs2439222	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439223	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439225	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439226	0.86[ASN][1000 genomes]
rs2439228	0.81[AMR][1000 genomes]
rs2439231	0.83[AMR][1000 genomes]
rs2439236	0.81[AMR][1000 genomes]
rs2448988	0.82[AMR][1000 genomes]
rs2448989	0.82[AMR][1000 genomes]
rs2448990	0.82[AMR][1000 genomes]
rs2448991	0.82[AMR][1000 genomes]
rs2448992	0.82[AMR][1000 genomes]
rs2449001	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449008	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2449009	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449011	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449012	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449014	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449016	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449017	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449019	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449020	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449021	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449022	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449023	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449026	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449027	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449028	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449029	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449030	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449031	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449034	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449035	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449036	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2449038	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2449039	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449040	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449041	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449042	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449055	0.82[AMR][1000 genomes]
rs2449058	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2449061	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2449062	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2449063	0.82[AMR][1000 genomes]
rs2449064	0.82[AMR][1000 genomes]
rs2449066	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2449067	0.82[AMR][1000 genomes]
rs2449070	0.81[AMR][1000 genomes]
rs2454673	0.86[ASN][1000 genomes]
rs2454680	0.84[ASN][1000 genomes]
rs2454682	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454684	0.82[ASN][1000 genomes]
rs2454685	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454686	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454691	0.87[ASN][1000 genomes]
rs2462197	0.82[AMR][1000 genomes]
rs2462198	0.82[AMR][1000 genomes]
rs2462199	0.82[AMR][1000 genomes]
rs2462200	0.82[AMR][1000 genomes]
rs2462219	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2462220	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2462221	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2462222	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2462227	0.82[AMR][1000 genomes]
rs2462230	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2462231	0.82[AMR][1000 genomes]
rs2462232	0.82[AMR][1000 genomes]
rs2462233	0.82[AMR][1000 genomes]
rs2462234	0.82[AMR][1000 genomes]
rs2462238	0.82[AMR][1000 genomes]
rs2462239	0.82[AMR][1000 genomes]
rs2462240	0.82[AMR][1000 genomes]
rs2462241	0.81[AMR][1000 genomes]
rs2462242	0.82[AMR][1000 genomes]
rs2462244	0.82[AMR][1000 genomes]
rs2470750	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2470751	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470752	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470753	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470754	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2470755	0.84[AMR][1000 genomes]
rs2470756	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470757	0.82[AMR][1000 genomes]
rs2470758	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470759	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2470760	0.82[AMR][1000 genomes]
rs2470762	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2470764	0.82[AMR][1000 genomes]
rs2470765	0.82[AMR][1000 genomes]
rs2470769	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470774	0.83[AMR][1000 genomes]
rs2470775	0.81[AMR][1000 genomes]
rs2470776	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470777	0.82[AMR][1000 genomes]
rs2470778	0.82[AMR][1000 genomes]
rs2470779	0.83[AMR][1000 genomes]
rs2470780	0.82[AMR][1000 genomes]
rs2470781	0.82[AMR][1000 genomes]
rs2470782	0.82[AMR][1000 genomes]
rs2470783	0.83[AMR][1000 genomes]
rs2470785	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2470786	0.81[AMR][1000 genomes]
rs2470787	0.83[AMR][1000 genomes]
rs2470788	0.82[AMR][1000 genomes]
rs2470790	0.83[AMR][1000 genomes]
rs2470793	0.82[AMR][1000 genomes]
rs2470796	0.83[AMR][1000 genomes]
rs2470797	0.83[AMR][1000 genomes]
rs2470798	0.82[AMR][1000 genomes]
rs2470808	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2470815	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470816	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470818	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470819	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2470821	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470822	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470823	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470824	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470825	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470826	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470829	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470830	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470831	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470833	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470836	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470840	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470842	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470843	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470844	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470845	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470846	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2470849	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470851	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2470852	0.81[ASN][1000 genomes]
rs2470854	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470857	0.82[ASN][1000 genomes]
rs2470859	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2470860	0.82[ASN][1000 genomes]
rs2470861	0.82[ASN][1000 genomes]
rs2470869	0.82[AMR][1000 genomes]
rs2470876	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470879	0.83[AMR][1000 genomes]
rs2470881	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470885	0.87[ASN][1000 genomes]
rs28608112	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929489	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2929490	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2949166	0.81[AMR][1000 genomes]
rs2960187	0.81[AMR][1000 genomes]
rs4241476	0.82[AMR][1000 genomes]
rs4241477	0.82[AMR][1000 genomes]
rs4450736	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276887	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440349	0.82[AMR][1000 genomes]
rs7630800	0.82[ASN][1000 genomes]
rs7631624	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633464	0.84[ASN][1000 genomes]
rs7635154	0.80[AMR][1000 genomes]
rs7648770	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9289683	0.86[ASN][1000 genomes]
rs9289685	0.87[ASN][1000 genomes]
rs951093	0.82[AMR][1000 genomes]
rs9821965	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9835142	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843864	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849048	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9852950	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857396	0.81[AMR][1000 genomes]
rs9860264	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9876797	0.81[AMR][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
rs6440280	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98705000-98713000	Weak transcription	HSMM	muscle
2	chr3:98705200-98712600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:98705400-98706400	Enhancers	A549	lung
4	chr3:98705400-98710400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:98705600-98716400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:98706200-98708000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:98706200-98712400	Weak transcription	NHDF-Ad	bronchial

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