Variant report

Variant	rs1039797
Chromosome Location	chr5:49651872-49651873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10041033	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10042504	0.89[ASN][1000 genomes]
rs10055539	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10056605	0.81[ASN][1000 genomes]
rs10061339	0.83[ASN][1000 genomes]
rs10066635	0.87[EUR][1000 genomes]
rs10068272	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10071725	0.91[ASN][1000 genomes]
rs10072182	0.80[ASN][1000 genomes]
rs10073530	0.80[ASN][1000 genomes]
rs10076490	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10079493	0.93[ASN][1000 genomes]
rs1010676	0.90[JPT][hapmap]
rs10471362	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471798	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10940129	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11959569	0.93[ASN][1000 genomes]
rs12513730	0.81[ASN][1000 genomes]
rs12651909	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13155292	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13157992	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13159506	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13173678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13174293	0.94[ASN][1000 genomes]
rs13180767	0.85[ASN][1000 genomes]
rs13180852	0.84[ASN][1000 genomes]
rs13182357	0.90[JPT][hapmap]
rs13185587	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1328254	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13357429	0.86[ASN][1000 genomes]
rs1344339	0.83[ASN][1000 genomes]
rs1511735	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1511737	0.82[ASN][1000 genomes]
rs1606226	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16879094	0.84[ASN][1000 genomes]
rs1811742	0.81[ASN][1000 genomes]
rs1812936	0.90[JPT][hapmap]
rs1812994	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1833900	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1849200	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1995795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2036902	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2089605	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2137129	0.80[ASN][1000 genomes]
rs2137132	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137134	1.00[ASN][1000 genomes]
rs2271236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2353436	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2668024	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28445612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28500170	0.84[ASN][1000 genomes]
rs28528780	0.84[ASN][1000 genomes]
rs28661824	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28676351	0.81[ASN][1000 genomes]
rs2883164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs303219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303231	0.85[ASN][1000 genomes]
rs303235	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs303237	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34044048	0.80[ASN][1000 genomes]
rs34044167	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34601168	0.83[ASN][1000 genomes]
rs34741488	0.91[ASN][1000 genomes]
rs34749302	0.86[ASN][1000 genomes]
rs34945845	0.83[ASN][1000 genomes]
rs35740733	0.84[ASN][1000 genomes]
rs36138717	0.83[ASN][1000 genomes]
rs3849669	0.93[ASN][1000 genomes]
rs3849670	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3860732	0.91[ASN][1000 genomes]
rs3950451	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4029989	0.83[ASN][1000 genomes]
rs4030569	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4030570	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4030571	0.91[ASN][1000 genomes]
rs4030572	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4030573	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4031137	0.90[ASN][1000 genomes]
rs4082836	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4145844	0.81[ASN][1000 genomes]
rs4337857	0.84[ASN][1000 genomes]
rs4340921	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4398636	0.89[ASN][1000 genomes]
rs4495185	0.86[ASN][1000 genomes]
rs4549528	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4571473	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4637546	0.95[ASN][1000 genomes]
rs4865522	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs507396	0.88[EUR][1000 genomes]
rs57137858	0.96[ASN][1000 genomes]
rs57583601	0.85[ASN][1000 genomes]
rs58756661	0.84[ASN][1000 genomes]
rs59254474	0.82[ASN][1000 genomes]
rs62365887	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62365896	0.87[ASN][1000 genomes]
rs62365901	0.86[ASN][1000 genomes]
rs62365902	0.83[ASN][1000 genomes]
rs62386175	0.89[ASN][1000 genomes]
rs6450056	0.95[ASN][1000 genomes]
rs6450063	0.91[ASN][1000 genomes]
rs6450098	0.86[ASN][1000 genomes]
rs6450099	0.83[ASN][1000 genomes]
rs6450107	0.85[ASN][1000 genomes]
rs6450139	0.84[ASN][1000 genomes]
rs6863840	0.83[ASN][1000 genomes]
rs6868677	0.82[ASN][1000 genomes]
rs6869871	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6871761	0.83[ASN][1000 genomes]
rs6874829	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876902	0.83[ASN][1000 genomes]
rs6877713	0.83[ASN][1000 genomes]
rs6897412	0.84[ASN][1000 genomes]
rs7442762	0.80[ASN][1000 genomes]
rs7442966	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7446360	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7712749	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7712849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7717982	0.83[ASN][1000 genomes]
rs7721808	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7730857	0.86[ASN][1000 genomes]
rs7732000	0.90[ASN][1000 genomes]
rs9292005	1.00[CHB][hapmap];1.00[JPT][hapmap];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	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	nsv965616	chr5:49642415-49658734	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
15	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1039797	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs1039797	EMB	cis	Thyroid	GTEx
rs1039797	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs1039797	EMB	cis	parietal	SCAN
rs1039797	ARL15	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49649600-49659000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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