Variant report

Variant	rs2352789
Chromosome Location	chr5:49550935-49550936
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10037889	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10038023	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10041903	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10042601	0.85[EUR][1000 genomes]
rs10051529	0.86[EUR][1000 genomes]
rs10056605	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10062032	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10068272	0.81[ASN][1000 genomes]
rs10071725	0.80[EUR][1000 genomes]
rs10072182	0.81[EUR][1000 genomes]
rs10073530	0.81[EUR][1000 genomes]
rs10074359	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1010676	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs1039798	0.81[EUR][1000 genomes]
rs10461390	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10461391	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10940129	0.81[ASN][1000 genomes]
rs11959569	0.80[EUR][1000 genomes]
rs12188175	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12513730	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12519021	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12697055	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13157992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13173678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13174293	0.82[EUR][1000 genomes]
rs13182357	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs1328254	0.92[ASN][1000 genomes]
rs13357429	0.90[CEU][hapmap]
rs1344339	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1511735	0.81[ASN][1000 genomes]
rs1511737	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1511738	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1606224	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1811742	1.00[CEU][hapmap]
rs1812936	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs2005573	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2011539	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2011540	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2036901	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2036902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2137129	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2137134	0.82[EUR][1000 genomes]
rs2168920	0.85[ASN][1000 genomes]
rs2199090	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2199092	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219451	0.83[ASN][1000 genomes]
rs2219452	0.84[ASN][1000 genomes]
rs2271236	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2668024	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28445612	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2883164	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs303219	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs34185098	0.83[EUR][1000 genomes]
rs34601168	0.83[EUR][1000 genomes]
rs35740733	0.85[EUR][1000 genomes]
rs3849669	0.80[EUR][1000 genomes]
rs4321782	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4331898	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4337857	0.85[EUR][1000 genomes]
rs4554275	0.83[ASN][1000 genomes]
rs4605784	0.84[EUR][1000 genomes]
rs4637546	0.82[EUR][1000 genomes]
rs471455	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs472278	0.80[ASN][1000 genomes]
rs481222	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs482120	0.83[ASN][1000 genomes]
rs485101	0.85[ASN][1000 genomes]
rs4865519	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4865522	0.81[ASN][1000 genomes]
rs4865698	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4865699	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4865700	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs494540	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs496108	0.88[ASN][1000 genomes]
rs498951	0.89[ASN][1000 genomes]
rs5011669	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs504520	0.87[ASN][1000 genomes]
rs506817	0.82[ASN][1000 genomes]
rs507396	0.92[ASN][1000 genomes]
rs527170	0.83[ASN][1000 genomes]
rs531198	0.86[ASN][1000 genomes]
rs534123	0.84[ASN][1000 genomes]
rs535100	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs535113	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs547563	0.86[ASN][1000 genomes]
rs552892	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs553798	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs559096	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs560861	0.85[ASN][1000 genomes]
rs57137858	0.80[EUR][1000 genomes]
rs58178891	0.83[EUR][1000 genomes]
rs58386948	0.80[ASN][1000 genomes]
rs6449961	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6450056	0.82[EUR][1000 genomes]
rs6863840	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6868380	0.85[EUR][1000 genomes]
rs6868721	1.00[CEU][hapmap]
rs6871761	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6876902	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6877713	0.86[EUR][1000 genomes]
rs6897412	0.85[EUR][1000 genomes]
rs7293426	0.84[ASN][1000 genomes]
rs7341010	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7442762	0.81[EUR][1000 genomes]
rs7446951	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7447926	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7712849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7722742	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8188210	0.85[ASN][1000 genomes]
rs9291925	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9292005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv820439	chr5:49405763-49552643	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv15107	chr5:49405763-49562327	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv2760950	chr5:49432831-49624358	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1028131	chr5:49455624-49552686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1017682	chr5:49455624-49556126	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1033820	chr5:49455624-49560281	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1025722	chr5:49455624-49561216	ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1016253	chr5:49455624-49564818	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1034447	chr5:49455624-49568948	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1015794	chr5:49455624-49572706	ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1021120	chr5:49455624-49583553	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1034906	chr5:49455624-49586503	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1016533	chr5:49455624-49587789	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1033970	chr5:49455624-49595874	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1032046	chr5:49455624-49597527	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1021477	chr5:49455624-49624358	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	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
18	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
19	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
20	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
21	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
22	esv3328813	chr5:49528095-49550993	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
23	esv3369422	chr5:49528095-49550993	ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
24	nsv598107	chr5:49530641-49560490	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
25	nsv1020912	chr5:49542837-49624358	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2352789	EMB	cis	Whole Blood	GTEx
rs2352789	EMB	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49546200-49552600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

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