Variant report

Variant	rs2254540
Chromosome Location	chr20:21949431-21949432
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 166 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1000334	0.83[EUR][1000 genomes]
rs1007169	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1014883	0.84[EUR][1000 genomes]
rs1014884	0.84[EUR][1000 genomes]
rs1014885	0.84[EUR][1000 genomes]
rs1155710	0.83[EUR][1000 genomes]
rs11699227	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13039748	0.83[EUR][1000 genomes]
rs1474928	0.80[EUR][1000 genomes]
rs1535199	0.83[EUR][1000 genomes]
rs1535200	0.83[EUR][1000 genomes]
rs1535201	0.83[EUR][1000 genomes]
rs1535202	0.83[EUR][1000 genomes]
rs1555264	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1555265	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs169311	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1884588	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1884589	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1884590	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1884595	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1980551	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980552	0.86[EUR][1000 genomes]
rs1980571	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1986765	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1988545	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998076	0.86[EUR][1000 genomes]
rs2009652	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2010733	0.83[EUR][1000 genomes]
rs201547	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs201548	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2016964	0.83[EUR][1000 genomes]
rs2024885	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2180438	0.84[EUR][1000 genomes]
rs2180439	0.85[EUR][1000 genomes]
rs2208050	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2208051	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2208052	0.83[EUR][1000 genomes]
rs2208054	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2208055	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2281526	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2328678	0.85[EUR][1000 genomes]
rs2328679	0.85[EUR][1000 genomes]
rs2328680	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2328681	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2328682	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2328683	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2328684	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424418	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424419	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424421	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424423	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424427	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2876614	0.83[EUR][1000 genomes]
rs3818179	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818180	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818181	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818182	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818183	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4390829	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4405823	0.83[EUR][1000 genomes]
rs4544515	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4815071	0.83[EUR][1000 genomes]
rs4815072	0.83[EUR][1000 genomes]
rs4815073	0.83[EUR][1000 genomes]
rs4815076	0.85[EUR][1000 genomes]
rs4815080	0.85[EUR][1000 genomes]
rs4815081	0.85[EUR][1000 genomes]
rs4815082	0.85[EUR][1000 genomes]
rs6035961	0.83[EUR][1000 genomes]
rs6035968	0.84[EUR][1000 genomes]
rs6035969	0.83[EUR][1000 genomes]
rs6035970	0.84[EUR][1000 genomes]
rs6035980	0.85[EUR][1000 genomes]
rs6035982	0.87[EUR][1000 genomes]
rs6035988	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6036003	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6036007	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6047660	0.83[EUR][1000 genomes]
rs6047661	0.83[EUR][1000 genomes]
rs6047662	0.82[EUR][1000 genomes]
rs6047663	0.83[EUR][1000 genomes]
rs6047676	0.83[EUR][1000 genomes]
rs6047677	0.84[EUR][1000 genomes]
rs6047679	0.84[EUR][1000 genomes]
rs6047681	0.84[EUR][1000 genomes]
rs6047682	0.85[EUR][1000 genomes]
rs6047683	0.85[EUR][1000 genomes]
rs6047684	0.85[EUR][1000 genomes]
rs6047691	0.84[EUR][1000 genomes]
rs6047692	0.85[EUR][1000 genomes]
rs6047694	0.85[EUR][1000 genomes]
rs6047705	0.85[EUR][1000 genomes]
rs6047709	0.87[EUR][1000 genomes]
rs6047713	0.87[EUR][1000 genomes]
rs6047714	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6047715	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6047728	0.81[AMR][1000 genomes]
rs6047729	0.80[EUR][1000 genomes]
rs6047730	0.81[EUR][1000 genomes]
rs6047731	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6047732	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6047733	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6047743	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6047744	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6047745	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6047748	0.93[EUR][1000 genomes]
rs6047749	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6047768	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047769	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6047798	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6047799	0.81[AMR][1000 genomes]
rs6075843	0.83[EUR][1000 genomes]
rs6075852	0.84[EUR][1000 genomes]
rs6075853	0.84[EUR][1000 genomes]
rs6075854	0.84[EUR][1000 genomes]
rs6075855	0.84[EUR][1000 genomes]
rs6075858	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6075861	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082524	0.83[EUR][1000 genomes]
rs6082525	0.83[EUR][1000 genomes]
rs6082533	0.84[EUR][1000 genomes]
rs6082540	0.85[EUR][1000 genomes]
rs6082541	0.84[EUR][1000 genomes]
rs6082553	0.85[EUR][1000 genomes]
rs6082556	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6082560	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6106421	0.83[EUR][1000 genomes]
rs6106434	0.88[ASN][1000 genomes]
rs6106438	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6113393	0.83[EUR][1000 genomes]
rs6113394	0.83[EUR][1000 genomes]
rs6113395	0.83[EUR][1000 genomes]
rs6113404	0.85[EUR][1000 genomes]
rs6113413	0.91[EUR][1000 genomes]
rs6113414	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6113415	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6113416	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6113418	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6113424	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6113425	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6113431	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6113435	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6113456	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137473	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137476	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6515191	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs718664	0.84[EUR][1000 genomes]
rs7261950	0.82[EUR][1000 genomes]
rs761890	0.85[EUR][1000 genomes]
rs761891	0.85[EUR][1000 genomes]
rs764777	0.83[EUR][1000 genomes]
rs8116929	0.83[EUR][1000 genomes]
rs8121238	0.84[EUR][1000 genomes]
rs8122229	0.83[EUR][1000 genomes]
rs927059	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs932540	0.85[EUR][1000 genomes]
rs966604	0.85[EUR][1000 genomes]
rs987050	0.84[EUR][1000 genomes]
rs997078	0.82[EUR][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	nsv1058137	chr20:21549350-22295051	Weak transcription Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv912815	chr20:21884693-21953649	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv585715	chr20:21906780-21951847	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv585716	chr20:21906780-21967950	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv585717	chr20:21917393-21949593	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
6	nsv458947	chr20:21917393-21961410	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
7	nsv585718	chr20:21917393-21961410	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:21949400-21951800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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