Variant report

Variant	rs13180767
Chromosome Location	chr5:49673770-49673771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 175 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10038023	0.82[EUR][1000 genomes]
rs10041033	0.92[ASN][1000 genomes]
rs10041903	0.84[EUR][1000 genomes]
rs10042504	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10042601	0.85[EUR][1000 genomes]
rs10043101	0.94[EUR][1000 genomes]
rs10051529	0.85[EUR][1000 genomes]
rs10055539	0.89[ASN][1000 genomes]
rs10056605	0.85[EUR][1000 genomes]
rs10060219	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10061339	0.86[ASN][1000 genomes]
rs10062032	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10071725	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10072182	0.91[EUR][1000 genomes]
rs10073530	0.90[EUR][1000 genomes]
rs10074359	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10076490	0.92[ASN][1000 genomes]
rs10079493	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1010676	0.87[EUR][1000 genomes]
rs1039797	0.85[ASN][1000 genomes]
rs1039798	0.91[EUR][1000 genomes]
rs10461390	0.84[EUR][1000 genomes]
rs10461391	0.85[EUR][1000 genomes]
rs10471362	0.87[ASN][1000 genomes]
rs10471798	0.82[ASN][1000 genomes]
rs11959569	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12109228	0.94[EUR][1000 genomes]
rs12188175	0.83[EUR][1000 genomes]
rs12513730	0.86[EUR][1000 genomes]
rs12651909	0.92[ASN][1000 genomes]
rs12659303	0.93[EUR][1000 genomes]
rs12697055	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13155292	0.92[ASN][1000 genomes]
rs13157992	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13159506	0.84[ASN][1000 genomes]
rs13173678	0.86[ASN][1000 genomes]
rs13174293	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13180579	0.95[EUR][1000 genomes]
rs13180852	0.87[ASN][1000 genomes]
rs13182357	0.90[EUR][1000 genomes]
rs13184466	0.86[EUR][1000 genomes]
rs13185587	0.87[ASN][1000 genomes]
rs13357429	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1344339	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1511737	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1511738	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1606224	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1606226	0.83[ASN][1000 genomes]
rs16879094	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1811742	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1812936	0.85[EUR][1000 genomes]
rs1812994	0.87[ASN][1000 genomes]
rs1849200	0.83[ASN][1000 genomes]
rs1995795	0.85[ASN][1000 genomes]
rs2005573	0.86[EUR][1000 genomes]
rs2011539	0.85[EUR][1000 genomes]
rs2011540	0.85[EUR][1000 genomes]
rs2036901	0.83[ASN][1000 genomes]
rs2036902	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2089605	0.87[ASN][1000 genomes]
rs2137129	0.86[EUR][1000 genomes]
rs2137132	0.85[ASN][1000 genomes]
rs2137134	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271236	0.84[ASN][1000 genomes]
rs2353436	0.83[ASN][1000 genomes]
rs2668024	0.85[ASN][1000 genomes]
rs28445612	0.84[ASN][1000 genomes]
rs28500170	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs28528780	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28661824	0.84[ASN][1000 genomes]
rs28676351	0.86[ASN][1000 genomes]
rs2883164	0.85[ASN][1000 genomes]
rs28842196	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs303219	0.84[ASN][1000 genomes]
rs303231	0.83[ASN][1000 genomes]
rs303235	0.87[ASN][1000 genomes]
rs303237	0.88[ASN][1000 genomes]
rs34044048	0.85[ASN][1000 genomes]
rs34044167	0.84[ASN][1000 genomes]
rs34185098	0.88[EUR][1000 genomes]
rs34601168	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34741488	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34749302	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34945845	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34950042	0.82[ASN][1000 genomes]
rs35740733	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35858778	0.87[EUR][1000 genomes]
rs35866059	0.82[EUR][1000 genomes]
rs36138717	0.81[ASN][1000 genomes]
rs3849669	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3849670	0.87[ASN][1000 genomes]
rs3860731	0.93[EUR][1000 genomes]
rs3860732	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3933097	0.95[EUR][1000 genomes]
rs3950451	0.92[ASN][1000 genomes]
rs4029989	0.87[ASN][1000 genomes]
rs4030569	0.93[ASN][1000 genomes]
rs4030570	0.93[ASN][1000 genomes]
rs4030571	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4030572	0.89[ASN][1000 genomes]
rs4030573	0.93[ASN][1000 genomes]
rs4031137	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4082836	0.84[ASN][1000 genomes]
rs4145844	0.84[ASN][1000 genomes]
rs4337857	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4340921	0.84[ASN][1000 genomes]
rs4398636	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4495185	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4549528	0.93[ASN][1000 genomes]
rs4571473	0.87[ASN][1000 genomes]
rs4605784	0.83[EUR][1000 genomes]
rs4637546	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs471455	0.83[EUR][1000 genomes]
rs4865519	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4865698	0.86[EUR][1000 genomes]
rs4865699	0.86[EUR][1000 genomes]
rs4865700	0.86[EUR][1000 genomes]
rs494540	0.83[EUR][1000 genomes]
rs5011669	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs552892	0.83[EUR][1000 genomes]
rs57137858	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57583601	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58178891	0.82[EUR][1000 genomes]
rs58756661	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs59254474	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62365887	0.84[ASN][1000 genomes]
rs62365896	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62365901	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62365902	0.80[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs62386175	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6449961	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6450056	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450063	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6450098	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6450099	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6450107	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6450139	0.87[ASN][1000 genomes]
rs6863840	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6868380	0.87[EUR][1000 genomes]
rs6868677	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6869871	0.87[ASN][1000 genomes]
rs6871761	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6874829	0.85[ASN][1000 genomes]
rs6876902	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6877713	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6897412	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7341010	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7442762	0.91[EUR][1000 genomes]
rs7446360	0.87[ASN][1000 genomes]
rs7446951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7447926	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7700537	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7712749	0.83[ASN][1000 genomes]
rs7712849	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7717982	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7721808	0.87[ASN][1000 genomes]
rs7722742	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7730857	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7732000	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9291925	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9292005	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9716734	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13180767	EMB	cis	Whole Blood	GTEx
rs13180767	EMB	cis	Thyroid	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49656400-49677800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr5:49659800-49678200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:49660400-49681800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr5:49661200-49683400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr5:49661600-49683000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:49664200-49683000	Weak transcription	Primary B cells from cord blood	blood
7	chr5:49665800-49682800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:49665800-49685000	Weak transcription	Spleen	Spleen
9	chr5:49666000-49682800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:49667800-49681600	Weak transcription	Primary T cells from cord blood	blood
11	chr5:49667800-49683000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr5:49668400-49677800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr5:49670000-49680200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:49670600-49683800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:49672600-49693800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:49673200-49682800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:49673200-49682800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:49673200-49683000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:49673400-49677600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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