Variant report

Variant	rs4946343
Chromosome Location	chr6:118718580-118718581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1016095	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10457334	0.83[ASN][1000 genomes]
rs10484287	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1051429	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10872163	0.85[ASN][1000 genomes]
rs11153735	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153737	0.85[ASN][1000 genomes]
rs11153738	0.85[ASN][1000 genomes]
rs12196194	0.80[ASN][1000 genomes]
rs12204456	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs12526557	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12530169	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs1344249	0.83[ASN][1000 genomes]
rs1547326	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1690673	0.82[EUR][1000 genomes]
rs172212	0.81[EUR][1000 genomes]
rs2181513	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2187945	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2213858	0.82[ASN][1000 genomes]
rs2356175	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2356178	0.99[ASN][1000 genomes]
rs2356179	0.85[ASN][1000 genomes]
rs2356180	0.85[ASN][1000 genomes]
rs2356182	0.83[ASN][1000 genomes]
rs2356184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2356493	0.82[ASN][1000 genomes]
rs25421	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs25423	0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs281869	0.86[CEU][hapmap]
rs283052	0.81[EUR][1000 genomes]
rs283083	0.81[CEU][hapmap]
rs2883849	0.86[CEU][hapmap]
rs3734382	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs3951041	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3951044	0.82[ASN][1000 genomes]
rs4027875	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4027876	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4027877	0.83[ASN][1000 genomes]
rs4027878	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4027881	0.85[ASN][1000 genomes]
rs4027883	0.85[ASN][1000 genomes]
rs422312	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4314526	0.81[ASN][1000 genomes]
rs4489189	0.84[ASN][1000 genomes]
rs4502975	0.85[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4568488	0.85[ASN][1000 genomes]
rs485416	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs492562	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs4946339	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4946349	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs516212	0.87[ASN][1000 genomes]
rs516463	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs541442	0.89[ASN][1000 genomes]
rs55868726	0.83[ASN][1000 genomes]
rs6569022	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6904968	0.85[ASN][1000 genomes]
rs6919887	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs6923888	0.85[ASN][1000 genomes]
rs6929390	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6936661	0.84[ASN][1000 genomes]
rs6937642	0.82[ASN][1000 genomes]
rs7740922	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7741644	0.86[JPT][hapmap]
rs7742696	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745692	0.85[ASN][1000 genomes]
rs7749208	0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7749694	0.85[JPT][hapmap]
rs7756973	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7757337	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7758933	0.85[ASN][1000 genomes]
rs7759088	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7761996	0.82[ASN][1000 genomes]
rs7766732	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7766907	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7769937	0.85[ASN][1000 genomes]
rs9285429	0.81[ASN][1000 genomes]
rs9320653	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs933257	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs9372506	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs9374733	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9374735	0.94[ASN][1000 genomes]
rs9374736	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs9387586	0.94[ASN][1000 genomes]
rs9401073	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9481790	0.84[ASN][1000 genomes]
rs9481795	0.82[ASN][1000 genomes]
rs9481807	0.83[ASN][1000 genomes]
rs9481815	0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9481819	0.86[JPT][hapmap]
rs9489368	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9489373	0.85[ASN][1000 genomes]
rs9489376	0.85[ASN][1000 genomes]
rs9489377	0.85[ASN][1000 genomes]
rs9489378	0.85[ASN][1000 genomes]
rs9489401	0.83[ASN][1000 genomes]
rs9489403	0.84[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9489406	0.82[ASN][1000 genomes]
rs9489414	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9489417	0.80[ASN][1000 genomes]
rs9489419	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9489420	0.86[JPT][hapmap]
rs9489424	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9489432	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9489437	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9489438	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9489439	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9489446	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs9489448	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs9489449	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs9717286	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830787	chr6:118631902-118805106	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv432958	chr6:118692307-119010307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv604555	chr6:118695049-118856822	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1034448	chr6:118698169-119016383	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv1020586	chr6:118711098-118900012	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
15	nsv432959	chr6:118716318-119010307	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946343	SSXP10	cis	Artery Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118707400-118729200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:118711200-118729000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:118712000-118727800	Weak transcription	Primary T cells from cord blood	blood
4	chr6:118715800-118731800	Weak transcription	Pancreas	Pancrea
5	chr6:118717000-118719000	Enhancers	Psoas Muscle	Psoas
6	chr6:118717400-118718600	Weak transcription	Fetal Heart	heart
7	chr6:118717400-118721800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:118718000-118718600	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr6:118718400-118719000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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