Variant report

Variant	rs6450099
Chromosome Location	chr5:49716047-49716048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 157 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10041033	0.88[ASN][1000 genomes]
rs10042504	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10043101	0.86[EUR][1000 genomes]
rs10055539	0.87[ASN][1000 genomes]
rs10059354	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10061339	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10062032	0.80[EUR][1000 genomes]
rs10071725	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10072182	0.83[EUR][1000 genomes]
rs10073530	0.83[EUR][1000 genomes]
rs10074359	0.80[EUR][1000 genomes]
rs10076490	0.93[ASN][1000 genomes]
rs10079493	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1010676	0.92[EUR][1000 genomes]
rs1016621	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1039797	0.83[ASN][1000 genomes]
rs1039798	0.83[EUR][1000 genomes]
rs10471362	0.86[ASN][1000 genomes]
rs10940334	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10940335	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10940336	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11948302	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11959569	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12109228	0.86[EUR][1000 genomes]
rs12651909	0.92[ASN][1000 genomes]
rs12659303	0.85[EUR][1000 genomes]
rs12697055	0.80[EUR][1000 genomes]
rs13153021	0.87[EUR][1000 genomes]
rs13155292	0.83[ASN][1000 genomes]
rs13157992	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13159506	0.92[ASN][1000 genomes]
rs13173678	0.92[ASN][1000 genomes]
rs13174293	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13180579	0.83[EUR][1000 genomes]
rs13180767	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13180852	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13182357	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13184466	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13184498	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13184661	0.82[EUR][1000 genomes]
rs13185587	0.86[ASN][1000 genomes]
rs13357429	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1344339	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1606224	0.80[EUR][1000 genomes]
rs1606226	0.88[ASN][1000 genomes]
rs16879094	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1811742	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1812936	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1812994	0.86[ASN][1000 genomes]
rs1833900	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1849200	0.88[ASN][1000 genomes]
rs1995795	0.83[ASN][1000 genomes]
rs2036901	0.90[ASN][1000 genomes]
rs2036902	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2089605	0.89[ASN][1000 genomes]
rs2137132	0.83[ASN][1000 genomes]
rs2137134	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2271236	0.89[ASN][1000 genomes]
rs2353436	0.88[ASN][1000 genomes]
rs2668024	0.93[ASN][1000 genomes]
rs28445612	0.89[ASN][1000 genomes]
rs28500170	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28528780	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28661824	0.89[ASN][1000 genomes]
rs28676351	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2883164	0.90[ASN][1000 genomes]
rs303219	0.91[ASN][1000 genomes]
rs303231	0.88[ASN][1000 genomes]
rs303235	0.85[ASN][1000 genomes]
rs303237	0.86[ASN][1000 genomes]
rs34044048	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34044167	0.90[ASN][1000 genomes]
rs34185098	0.81[EUR][1000 genomes]
rs34433187	0.86[EUR][1000 genomes]
rs34601168	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34741488	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34749302	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34774804	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34945845	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34950042	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35740733	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35858778	0.94[EUR][1000 genomes]
rs35866059	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36138717	0.86[ASN][1000 genomes]
rs3849669	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3849670	0.86[ASN][1000 genomes]
rs3860731	0.85[EUR][1000 genomes]
rs3860732	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3933097	0.84[EUR][1000 genomes]
rs3950451	0.90[ASN][1000 genomes]
rs4029989	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4030569	0.92[ASN][1000 genomes]
rs4030570	0.92[ASN][1000 genomes]
rs4030571	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4030572	0.87[ASN][1000 genomes]
rs4030573	0.91[ASN][1000 genomes]
rs4031137	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4082836	0.89[ASN][1000 genomes]
rs4145844	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4277861	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4337857	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4398636	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4495185	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4549528	0.92[ASN][1000 genomes]
rs4571473	0.85[ASN][1000 genomes]
rs4637546	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57137858	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57583601	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58756661	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59254474	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62365887	0.91[ASN][1000 genomes]
rs62365896	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62365901	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62365902	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62386175	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6450056	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6450063	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450098	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6450107	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6450139	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6860503	0.88[EUR][1000 genomes]
rs6863840	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6868380	0.80[EUR][1000 genomes]
rs6868677	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6869871	0.89[ASN][1000 genomes]
rs6871761	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6874829	0.83[ASN][1000 genomes]
rs6876902	0.80[EUR][1000 genomes]
rs6877713	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6897412	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7341010	0.80[EUR][1000 genomes]
rs7442762	0.83[EUR][1000 genomes]
rs7446360	0.89[ASN][1000 genomes]
rs7446951	0.80[EUR][1000 genomes]
rs7706105	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7712749	0.90[ASN][1000 genomes]
rs7712849	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7717982	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7719081	0.81[EUR][1000 genomes]
rs7721808	0.86[ASN][1000 genomes]
rs7722742	0.80[EUR][1000 genomes]
rs7730857	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7732000	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9291925	0.80[EUR][1000 genomes]
rs9292005	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9716734	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6450099	EMB	cis	Thyroid	GTEx
rs6450099	EMB	cis	Whole Blood	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49682000-49719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:49697400-49723400	Weak transcription	HSMM	muscle
5	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr5:49703200-49719000	Weak transcription	HMEC	breast
8	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:49709600-49716800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:49712200-49718200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:49712200-49718600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:49712800-49716200	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr5:49713000-49716200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr5:49713000-49719600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:49713000-49722000	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:49713000-49722600	Weak transcription	Fetal Thymus	thymus
18	chr5:49713000-49725800	Weak transcription	Small Intestine	intestine
19	chr5:49713200-49716200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:49714600-49718800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr5:49714800-49721200	Weak transcription	Primary T cells from cord blood	blood
22	chr5:49715000-49716200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:49715000-49716200	Weak transcription	Dnd41	blood
24	chr5:49715000-49716600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:49715000-49718600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:49715000-49722600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:49715000-49723400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr5:49715000-49723800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:49715200-49716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:49715400-49716600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:49715400-49717000	Strong transcription	Primary B cells from cord blood	blood
32	chr5:49715600-49718000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:49715800-49716600	Enhancers	Fetal Intestine Large	intestine
34	chr5:49715800-49717000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr5:49716000-49717000	Genic enhancers	Primary neutrophils fromperipheralblood	blood

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