Variant report

Variant	rs3849670
Chromosome Location	chr5:49661475-49661476
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10041033	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10042504	0.91[ASN][1000 genomes]
rs10055539	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10056605	0.83[ASN][1000 genomes]
rs10059354	0.80[ASN][1000 genomes]
rs10061339	0.85[ASN][1000 genomes]
rs10062032	0.80[ASN][1000 genomes]
rs10066635	0.85[EUR][1000 genomes]
rs10068272	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10071725	0.94[ASN][1000 genomes]
rs10074359	0.80[ASN][1000 genomes]
rs10076490	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10079493	0.95[ASN][1000 genomes]
rs1010676	0.83[JPT][hapmap]
rs1039797	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10461391	0.82[ASN][1000 genomes]
rs10471362	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471798	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10940129	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11948752	0.81[ASN][1000 genomes]
rs11959569	0.95[ASN][1000 genomes]
rs12513730	0.83[ASN][1000 genomes]
rs12651909	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12659303	0.80[ASN][1000 genomes]
rs12697055	0.80[ASN][1000 genomes]
rs13155292	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13157992	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs13159506	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13173678	0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13174293	0.91[ASN][1000 genomes]
rs13180767	0.87[ASN][1000 genomes]
rs13180852	0.87[ASN][1000 genomes]
rs13185587	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328254	0.88[EUR][1000 genomes]
rs13357429	0.89[ASN][1000 genomes]
rs1344339	0.85[ASN][1000 genomes]
rs1511735	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1511737	0.85[ASN][1000 genomes]
rs1511738	0.80[ASN][1000 genomes]
rs1606226	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16879094	0.87[ASN][1000 genomes]
rs1811742	0.83[ASN][1000 genomes]
rs1812994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1833900	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1849200	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1962832	0.81[ASN][1000 genomes]
rs1995795	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2036901	0.83[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2036902	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2089605	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2137129	0.83[ASN][1000 genomes]
rs2137132	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2137134	0.97[ASN][1000 genomes]
rs2271236	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2353436	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2668024	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28445612	0.87[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28500170	0.87[ASN][1000 genomes]
rs28528780	0.87[ASN][1000 genomes]
rs28661824	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28676351	0.84[ASN][1000 genomes]
rs2883164	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs303219	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs303231	0.87[ASN][1000 genomes]
rs303235	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303237	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34044048	0.83[ASN][1000 genomes]
rs34044167	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34601168	0.85[ASN][1000 genomes]
rs34741488	0.94[ASN][1000 genomes]
rs34749302	0.89[ASN][1000 genomes]
rs34945845	0.85[ASN][1000 genomes]
rs34950042	0.81[ASN][1000 genomes]
rs35740733	0.87[ASN][1000 genomes]
rs36138717	0.85[ASN][1000 genomes]
rs3849669	0.95[ASN][1000 genomes]
rs3860732	0.94[ASN][1000 genomes]
rs3950451	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4029989	0.86[ASN][1000 genomes]
rs4030569	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4030570	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4030571	0.94[ASN][1000 genomes]
rs4030572	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4030573	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4031137	0.93[ASN][1000 genomes]
rs4082836	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4145844	0.84[ASN][1000 genomes]
rs4337857	0.87[ASN][1000 genomes]
rs4340921	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4398636	0.91[ASN][1000 genomes]
rs4495185	0.89[ASN][1000 genomes]
rs4549528	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4563580	0.81[ASN][1000 genomes]
rs4571473	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637546	0.93[ASN][1000 genomes]
rs4865522	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5011669	0.80[ASN][1000 genomes]
rs507396	0.85[EUR][1000 genomes]
rs57137858	0.99[ASN][1000 genomes]
rs57583601	0.87[ASN][1000 genomes]
rs58756661	0.87[ASN][1000 genomes]
rs59254474	0.85[ASN][1000 genomes]
rs62365887	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62365896	0.89[ASN][1000 genomes]
rs62365901	0.88[ASN][1000 genomes]
rs62365902	0.85[ASN][1000 genomes]
rs62386175	0.92[ASN][1000 genomes]
rs6449961	0.81[ASN][1000 genomes]
rs6450056	0.92[ASN][1000 genomes]
rs6450063	0.94[ASN][1000 genomes]
rs6450098	0.89[ASN][1000 genomes]
rs6450099	0.86[ASN][1000 genomes]
rs6450107	0.87[ASN][1000 genomes]
rs6450139	0.87[ASN][1000 genomes]
rs6450164	0.81[ASN][1000 genomes]
rs6863840	0.85[ASN][1000 genomes]
rs6868677	0.85[ASN][1000 genomes]
rs6869871	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6871761	0.85[ASN][1000 genomes]
rs6874829	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6876902	0.86[ASN][1000 genomes]
rs6877713	0.85[ASN][1000 genomes]
rs6897412	0.87[ASN][1000 genomes]
rs7341010	0.80[ASN][1000 genomes]
rs7442966	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7446360	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7446951	0.80[ASN][1000 genomes]
rs7447926	0.80[ASN][1000 genomes]
rs7712749	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7712849	0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7717982	0.85[ASN][1000 genomes]
rs7721808	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722742	0.81[ASN][1000 genomes]
rs7730857	0.87[ASN][1000 genomes]
rs7732000	0.93[ASN][1000 genomes]
rs9291925	0.81[ASN][1000 genomes]
rs9292005	0.83[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019539	chr5:49455624-49702736	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS 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	5 gene(s)	inside rSNPs	diseases
4	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv4818	chr5:49647989-49661497	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3849670	EMB	cis	Thyroid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49652800-49665400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:49656400-49661800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr5:49656400-49677800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:49658800-49661600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr5:49658800-49662000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr5:49658800-49662200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:49658800-49662200	Enhancers	Dnd41	blood
8	chr5:49659000-49662200	Enhancers	Primary hematopoietic stem cells	blood
9	chr5:49659200-49662200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:49659400-49661600	Weak transcription	Primary B cells from cord blood	blood
11	chr5:49659800-49678200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:49660400-49681800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:49660600-49662000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:49660800-49662000	Enhancers	Adipose Nuclei	Adipose
15	chr5:49660800-49672400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr5:49661000-49661600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:49661000-49665800	Weak transcription	Primary T cells from cord blood	blood
18	chr5:49661000-49667400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:49661200-49662000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:49661200-49662200	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr5:49661200-49683400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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