Variant report

Variant	rs10940129
Chromosome Location	chr5:49611091-49611092
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10037889	0.87[ASN][1000 genomes]
rs10038023	0.86[ASN][1000 genomes]
rs10041033	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10041903	0.87[ASN][1000 genomes]
rs10042601	0.80[ASN][1000 genomes]
rs10055539	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10056605	0.99[ASN][1000 genomes]
rs10062032	0.95[ASN][1000 genomes]
rs10066635	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10068272	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074359	0.95[ASN][1000 genomes]
rs10076490	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10079493	0.80[ASN][1000 genomes]
rs1039797	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10461390	0.92[ASN][1000 genomes]
rs10461391	0.97[ASN][1000 genomes]
rs10461519	0.86[ASN][1000 genomes]
rs10471362	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10471798	0.84[EUR][1000 genomes]
rs11959569	0.80[ASN][1000 genomes]
rs12188175	0.92[ASN][1000 genomes]
rs12513730	0.99[ASN][1000 genomes]
rs12651909	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12697055	0.95[ASN][1000 genomes]
rs13155292	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13159506	0.81[EUR][1000 genomes]
rs13185587	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1328254	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1344339	0.90[ASN][1000 genomes]
rs1511735	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511737	1.00[ASN][1000 genomes]
rs1511738	0.95[ASN][1000 genomes]
rs1606224	0.95[ASN][1000 genomes]
rs1812994	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1995795	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2005573	0.89[ASN][1000 genomes]
rs2011539	0.89[ASN][1000 genomes]
rs2011540	0.89[ASN][1000 genomes]
rs2036901	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2089605	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2137129	0.98[ASN][1000 genomes]
rs2137132	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2137134	0.82[ASN][1000 genomes]
rs2271236	0.82[EUR][1000 genomes]
rs2352789	0.81[ASN][1000 genomes]
rs2668024	0.80[EUR][1000 genomes]
rs2883164	0.82[EUR][1000 genomes]
rs303219	0.82[EUR][1000 genomes]
rs303235	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303237	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34044167	0.83[EUR][1000 genomes]
rs34601168	0.87[ASN][1000 genomes]
rs35740733	0.89[ASN][1000 genomes]
rs3849669	0.80[ASN][1000 genomes]
rs3849670	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3950451	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4030569	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4030570	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4030572	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4030573	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4321782	0.81[ASN][1000 genomes]
rs4331898	0.90[ASN][1000 genomes]
rs4337857	0.89[ASN][1000 genomes]
rs4340921	0.80[AMR][1000 genomes]
rs4549528	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4571473	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs471455	0.87[ASN][1000 genomes]
rs481222	0.85[ASN][1000 genomes]
rs4865519	0.90[ASN][1000 genomes]
rs4865522	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865698	0.94[ASN][1000 genomes]
rs4865699	0.94[ASN][1000 genomes]
rs4865700	0.94[ASN][1000 genomes]
rs494540	0.87[ASN][1000 genomes]
rs498951	0.81[EUR][1000 genomes]
rs5011669	0.95[ASN][1000 genomes]
rs507396	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs552892	0.82[ASN][1000 genomes]
rs57137858	0.83[ASN][1000 genomes]
rs58386948	0.87[ASN][1000 genomes]
rs62365887	0.83[EUR][1000 genomes]
rs6449961	0.94[ASN][1000 genomes]
rs6863840	0.90[ASN][1000 genomes]
rs6869871	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6871761	0.90[ASN][1000 genomes]
rs6874829	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6876902	0.99[ASN][1000 genomes]
rs6877713	0.87[ASN][1000 genomes]
rs6897412	0.89[ASN][1000 genomes]
rs7341010	0.95[ASN][1000 genomes]
rs7442966	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7446360	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7446951	0.95[ASN][1000 genomes]
rs7447926	0.95[ASN][1000 genomes]
rs7712749	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7721808	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7722742	0.94[ASN][1000 genomes]
rs9291925	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv1020912	chr5:49542837-49624358	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10940129	EMB	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49602600-49615800	Weak transcription	Dnd41	blood

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