Variant report

Variant	rs6539919
Chromosome Location	chr12:86151717-86151718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 168 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10506920	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10506921	0.86[ASN][1000 genomes]
rs10506922	0.93[ASN][1000 genomes]
rs10506923	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10735486	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10746353	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10779201	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10779202	0.93[ASN][1000 genomes]
rs10779203	0.93[ASN][1000 genomes]
rs10779204	0.93[ASN][1000 genomes]
rs10779206	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10779207	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10779208	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10779210	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10863069	0.93[ASN][1000 genomes]
rs10863070	0.93[ASN][1000 genomes]
rs10863071	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10863073	0.93[ASN][1000 genomes]
rs10863075	0.93[ASN][1000 genomes]
rs10863076	0.93[ASN][1000 genomes]
rs10863077	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10863078	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10863079	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10863080	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11117016	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11117017	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11117019	0.90[ASN][1000 genomes]
rs11117020	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11117021	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11117023	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11608717	0.80[ASN][1000 genomes]
rs11608719	0.80[ASN][1000 genomes]
rs11609351	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11610120	0.80[ASN][1000 genomes]
rs11610371	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11610627	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11610763	0.80[ASN][1000 genomes]
rs11610789	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11610846	0.93[ASN][1000 genomes]
rs11611968	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11612432	0.80[ASN][1000 genomes]
rs11612928	0.80[ASN][1000 genomes]
rs11612938	0.80[ASN][1000 genomes]
rs11613070	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11614513	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11615116	0.93[ASN][1000 genomes]
rs11830880	0.80[ASN][1000 genomes]
rs11831936	0.80[ASN][1000 genomes]
rs12309130	0.93[ASN][1000 genomes]
rs12426417	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12829972	0.80[ASN][1000 genomes]
rs17279133	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17279205	0.86[ASN][1000 genomes]
rs17279240	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17279261	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17279289	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17279338	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17279464	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17279916	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17344633	0.93[ASN][1000 genomes]
rs17344834	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17345028	0.86[ASN][1000 genomes]
rs17345272	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17345299	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17345522	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2061686	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2199519	0.93[ASN][1000 genomes]
rs2199520	0.93[ASN][1000 genomes]
rs2219715	0.93[ASN][1000 genomes]
rs2405613	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2405614	0.93[ASN][1000 genomes]
rs2405615	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405621	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405623	0.82[EUR][1000 genomes]
rs34555363	0.80[ASN][1000 genomes]
rs34656916	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34885805	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35034633	0.80[ASN][1000 genomes]
rs35648674	0.80[ASN][1000 genomes]
rs36046732	0.80[ASN][1000 genomes]
rs4278581	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4278582	0.93[ASN][1000 genomes]
rs4326880	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4341613	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4393398	0.93[ASN][1000 genomes]
rs4412812	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4462416	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4559760	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4897818	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4897823	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4897827	0.93[ASN][1000 genomes]
rs4897828	0.93[ASN][1000 genomes]
rs4897829	0.86[ASN][1000 genomes]
rs4897830	0.80[ASN][1000 genomes]
rs4897831	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4897834	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4897844	0.93[ASN][1000 genomes]
rs56135828	0.80[ASN][1000 genomes]
rs56291271	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56330110	0.80[ASN][1000 genomes]
rs58742237	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59858864	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60539006	0.80[ASN][1000 genomes]
rs60947649	0.80[ASN][1000 genomes]
rs61928899	0.80[ASN][1000 genomes]
rs61928905	0.80[ASN][1000 genomes]
rs61928906	0.80[ASN][1000 genomes]
rs61928907	0.80[ASN][1000 genomes]
rs61930029	0.86[ASN][1000 genomes]
rs61930035	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930036	0.86[ASN][1000 genomes]
rs61930037	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930575	0.93[ASN][1000 genomes]
rs61930577	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61930579	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930580	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930581	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930582	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930585	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930586	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930587	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930588	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930589	0.93[ASN][1000 genomes]
rs61930590	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61930591	0.93[ASN][1000 genomes]
rs61930624	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61930625	0.80[ASN][1000 genomes]
rs61930626	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61930629	0.80[ASN][1000 genomes]
rs61930631	0.80[ASN][1000 genomes]
rs61930632	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61930633	0.80[ASN][1000 genomes]
rs61930637	0.80[ASN][1000 genomes]
rs61930639	0.80[ASN][1000 genomes]
rs61930640	0.80[ASN][1000 genomes]
rs61930641	0.80[ASN][1000 genomes]
rs61930644	0.80[ASN][1000 genomes]
rs6539921	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66656505	0.80[ASN][1000 genomes]
rs67914794	0.80[ASN][1000 genomes]
rs7136905	0.93[ASN][1000 genomes]
rs7137041	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307617	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7307626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7314668	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73174576	0.80[ASN][1000 genomes]
rs73176549	0.80[ASN][1000 genomes]
rs7399276	0.80[ASN][1000 genomes]
rs7399277	0.80[ASN][1000 genomes]
rs7954472	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7959372	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968059	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7976647	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7979156	0.80[ASN][1000 genomes]
rs974816	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974817	0.93[ASN][1000 genomes]
rs974818	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9788214	0.80[ASN][1000 genomes]
rs9788252	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1052187	chr12:85954455-86278200	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv541560	chr12:85954455-86278200	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1054475	chr12:85985510-86175711	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541561	chr12:85985510-86175711	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv455680	chr12:86120810-86160277	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	n/a	n/a	inside rSNPs	diseases
9	nsv559666	chr12:86120810-86160277	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	n/a	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86150400-86152800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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