Variant report

Variant	rs6549689
Chromosome Location	chr3:75134197-75134198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FRG2C-13	chr3:75133306-75134388	NONHSAT090497

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11709921	0.81[ASN][1000 genomes]
rs11920209	0.81[ASN][1000 genomes]
rs12054293	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12054432	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12171270	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486094	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12488229	0.89[CEU][hapmap];0.95[JPT][hapmap]
rs12492862	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12494321	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496883	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629483	0.91[ASN][1000 genomes]
rs12632116	0.91[ASN][1000 genomes]
rs12632660	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12636203	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12636209	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13065802	0.80[EUR][1000 genomes]
rs4073454	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4076158	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4076688	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234198	0.82[EUR][1000 genomes]
rs4298078	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4349537	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4356853	0.84[ASN][1000 genomes]
rs4361306	0.82[EUR][1000 genomes]
rs4368539	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4449358	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4467494	0.80[ASN][1000 genomes]
rs4544657	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4589972	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4607148	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4635750	0.84[ASN][1000 genomes]
rs4676991	0.87[EUR][1000 genomes]
rs4676992	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4677447	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4677449	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4677458	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4677473	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4677474	0.88[EUR][1000 genomes]
rs5009222	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57194478	0.88[EUR][1000 genomes]
rs59643911	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59715156	0.88[EUR][1000 genomes]
rs62258901	0.84[ASN][1000 genomes]
rs62260995	0.86[EUR][1000 genomes]
rs62260996	0.85[EUR][1000 genomes]
rs62261003	0.81[EUR][1000 genomes]
rs62261005	0.82[EUR][1000 genomes]
rs62261007	0.82[EUR][1000 genomes]
rs62261010	0.82[EUR][1000 genomes]
rs6549681	0.81[ASN][1000 genomes]
rs6549685	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6549700	0.88[EUR][1000 genomes]
rs6761963	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6777388	0.89[EUR][1000 genomes]
rs6796018	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6800028	0.89[EUR][1000 genomes]
rs72628656	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7429585	0.88[EUR][1000 genomes]
rs7429678	0.85[EUR][1000 genomes]
rs7430106	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431394	0.84[EUR][1000 genomes]
rs7432426	0.81[EUR][1000 genomes]
rs7616253	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7651120	0.82[EUR][1000 genomes]
rs7652902	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9310311	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9810161	0.85[EUR][1000 genomes]
rs9815881	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816018	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825398	0.81[ASN][1000 genomes]
rs9833132	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9835668	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842069	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9845814	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850353	0.91[ASN][1000 genomes]
rs9863946	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9865292	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9868696	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9869924	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9877977	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881282	0.81[ASN][1000 genomes]
rs9882460	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529994	chr3:74720752-75471887	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv916594	chr3:74943399-75540161	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv1851336	chr3:74970564-75280989	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1005139	chr3:75027834-75168557	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv534344	chr3:75028665-75164716	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834736	chr3:75083055-75271458	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	esv2760746	chr3:75119190-75140739	Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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