Variant report

Variant	rs1123293
Chromosome Location	chr3:98686064-98686065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 237 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:232)

rs_ID	r²[population]
rs12054181	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383902	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1383903	0.87[AMR][1000 genomes]
rs1383904	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1383905	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383910	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1481634	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481635	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481636	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1481637	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524227	0.84[AMR][1000 genomes]
rs1524228	0.84[AMR][1000 genomes]
rs1524229	0.84[AMR][1000 genomes]
rs1580372	0.84[AMR][1000 genomes]
rs1580374	0.86[AMR][1000 genomes]
rs1580375	0.83[AMR][1000 genomes]
rs1580376	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1585984	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1585985	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1585986	0.84[AMR][1000 genomes]
rs1585988	0.83[AMR][1000 genomes]
rs1837500	0.86[ASN][1000 genomes]
rs1875086	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1905015	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1905016	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1905017	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1905018	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1905019	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1905020	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1905021	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1967009	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028393	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062059	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2062060	0.86[AMR][1000 genomes]
rs2062061	0.86[AMR][1000 genomes]
rs2119187	0.82[ASN][1000 genomes]
rs2119188	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2128048	0.86[AMR][1000 genomes]
rs2128049	0.86[AMR][1000 genomes]
rs2128050	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2128051	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2128054	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246861	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249740	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2262597	0.84[AMR][1000 genomes]
rs2262598	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2262599	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2262600	0.83[AMR][1000 genomes]
rs2262602	0.83[AMR][1000 genomes]
rs2262603	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2439213	0.84[AMR][1000 genomes]
rs2439215	0.81[AMR][1000 genomes]
rs2439218	0.84[AMR][1000 genomes]
rs2439220	0.82[ASN][1000 genomes]
rs2439222	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439223	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439225	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439226	0.86[ASN][1000 genomes]
rs2439228	0.84[AMR][1000 genomes]
rs2439231	0.85[AMR][1000 genomes]
rs2439236	0.84[AMR][1000 genomes]
rs2448988	0.84[AMR][1000 genomes]
rs2448989	0.84[AMR][1000 genomes]
rs2448990	0.84[AMR][1000 genomes]
rs2448991	0.84[AMR][1000 genomes]
rs2448992	0.84[AMR][1000 genomes]
rs2449001	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449008	0.86[AMR][1000 genomes]
rs2449009	0.86[AMR][1000 genomes]
rs2449011	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449012	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449014	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449016	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449017	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449019	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449020	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449021	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449022	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449023	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449026	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449027	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449028	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449029	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449030	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449031	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449034	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449035	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449036	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2449038	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2449039	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449040	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449041	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449042	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2449055	0.84[AMR][1000 genomes]
rs2449058	0.86[AMR][1000 genomes]
rs2449061	0.86[AMR][1000 genomes]
rs2449062	0.86[AMR][1000 genomes]
rs2449063	0.84[AMR][1000 genomes]
rs2449064	0.84[AMR][1000 genomes]
rs2449065	0.82[AMR][1000 genomes]
rs2449066	0.86[AMR][1000 genomes]
rs2449067	0.84[AMR][1000 genomes]
rs2449070	0.83[AMR][1000 genomes]
rs2454673	0.86[ASN][1000 genomes]
rs2454680	0.84[ASN][1000 genomes]
rs2454682	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454684	0.82[ASN][1000 genomes]
rs2454685	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454686	0.89[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454691	0.87[ASN][1000 genomes]
rs2462197	0.84[AMR][1000 genomes]
rs2462198	0.84[AMR][1000 genomes]
rs2462199	0.84[AMR][1000 genomes]
rs2462200	0.84[AMR][1000 genomes]
rs2462219	0.86[AMR][1000 genomes]
rs2462220	0.86[AMR][1000 genomes]
rs2462221	0.86[AMR][1000 genomes]
rs2462222	0.83[AMR][1000 genomes]
rs2462227	0.84[AMR][1000 genomes]
rs2462230	0.86[AMR][1000 genomes]
rs2462231	0.84[AMR][1000 genomes]
rs2462232	0.84[AMR][1000 genomes]
rs2462233	0.84[AMR][1000 genomes]
rs2462234	0.84[AMR][1000 genomes]
rs2462235	0.82[AMR][1000 genomes]
rs2462236	0.82[AMR][1000 genomes]
rs2462237	0.82[AMR][1000 genomes]
rs2462238	0.84[AMR][1000 genomes]
rs2462239	0.84[AMR][1000 genomes]
rs2462240	0.84[AMR][1000 genomes]
rs2462241	0.83[AMR][1000 genomes]
rs2462242	0.84[AMR][1000 genomes]
rs2462244	0.84[AMR][1000 genomes]
rs2470750	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470751	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470752	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470753	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470754	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2470755	0.86[AMR][1000 genomes]
rs2470756	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470757	0.84[AMR][1000 genomes]
rs2470758	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470759	0.86[AMR][1000 genomes]
rs2470760	0.84[AMR][1000 genomes]
rs2470762	0.86[AMR][1000 genomes]
rs2470764	0.84[AMR][1000 genomes]
rs2470765	0.84[AMR][1000 genomes]
rs2470769	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470774	0.86[AMR][1000 genomes]
rs2470775	0.83[AMR][1000 genomes]
rs2470776	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470777	0.84[AMR][1000 genomes]
rs2470778	0.84[AMR][1000 genomes]
rs2470779	0.86[AMR][1000 genomes]
rs2470780	0.84[AMR][1000 genomes]
rs2470781	0.84[AMR][1000 genomes]
rs2470782	0.84[AMR][1000 genomes]
rs2470783	0.86[AMR][1000 genomes]
rs2470784	0.81[AMR][1000 genomes]
rs2470785	0.86[AMR][1000 genomes]
rs2470786	0.83[AMR][1000 genomes]
rs2470787	0.86[AMR][1000 genomes]
rs2470788	0.84[AMR][1000 genomes]
rs2470790	0.86[AMR][1000 genomes]
rs2470793	0.84[AMR][1000 genomes]
rs2470796	0.86[AMR][1000 genomes]
rs2470797	0.86[AMR][1000 genomes]
rs2470798	0.84[AMR][1000 genomes]
rs2470808	0.86[AMR][1000 genomes]
rs2470815	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470816	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470818	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470819	0.86[AMR][1000 genomes]
rs2470821	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470822	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470823	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470824	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470825	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470826	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470829	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470830	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470831	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470832	0.81[AMR][1000 genomes]
rs2470833	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470836	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470840	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470842	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470843	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470844	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470845	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470846	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2470849	0.87[AMR][1000 genomes]
rs2470851	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2470852	0.81[ASN][1000 genomes]
rs2470854	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2470857	0.82[ASN][1000 genomes]
rs2470859	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2470860	0.82[ASN][1000 genomes]
rs2470861	0.82[ASN][1000 genomes]
rs2470869	0.84[AMR][1000 genomes]
rs2470876	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470879	0.85[AMR][1000 genomes]
rs2470881	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470885	0.87[ASN][1000 genomes]
rs28608112	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2929489	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2929490	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2949166	0.83[AMR][1000 genomes]
rs2960187	0.83[AMR][1000 genomes]
rs2960190	0.82[EUR][1000 genomes]
rs4241476	0.84[AMR][1000 genomes]
rs4241477	0.84[AMR][1000 genomes]
rs4450736	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276887	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440280	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440349	0.84[AMR][1000 genomes]
rs7630800	0.82[ASN][1000 genomes]
rs7631624	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633464	0.84[ASN][1000 genomes]
rs7635154	0.83[AMR][1000 genomes]
rs7648770	0.87[AMR][1000 genomes]
rs9289683	0.86[ASN][1000 genomes]
rs9289685	0.87[ASN][1000 genomes]
rs951093	0.84[AMR][1000 genomes]
rs9821965	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9835142	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843864	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849048	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9852950	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857396	0.83[AMR][1000 genomes]
rs9860264	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9876797	0.83[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
rs1123293	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98683400-98687600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:98683800-98690000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:98684200-98686200	Weak transcription	NHLF	lung
4	chr3:98684400-98690200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:98684400-98690200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:98684800-98689400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:98685200-98687400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:98685200-98690400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:98685200-98690400	Enhancers	HUVEC	blood vessel
10	chr3:98685400-98688000	Enhancers	Osteobl	bone
11	chr3:98685600-98686400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:98685600-98686400	Flanking Active TSS	NHEK	skin
13	chr3:98685600-98686600	Flanking Active TSS	NH-A	brain
14	chr3:98685800-98686200	Enhancers	HSMM	muscle
15	chr3:98685800-98686400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:98685800-98686400	Flanking Active TSS	HMEC	breast
17	chr3:98685800-98687000	Flanking Active TSS	NHDF-Ad	bronchial
18	chr3:98685800-98687200	Active TSS	A549	lung
19	chr3:98685800-98687600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:98686000-98686800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:98686000-98687200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:98686000-98687600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:98686000-98687800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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