Variant report

Variant	rs13039748
Chromosome Location	chr20:21820041-21820042
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 155 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs1000334	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1007169	0.83[EUR][1000 genomes]
rs1014883	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014884	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1014885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155710	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11696707	0.89[ASN][1000 genomes]
rs11699227	0.82[EUR][1000 genomes]
rs1474928	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535199	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535200	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1535201	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535202	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555264	0.82[EUR][1000 genomes]
rs1555265	0.82[EUR][1000 genomes]
rs169311	0.82[EUR][1000 genomes]
rs1884588	0.87[EUR][1000 genomes]
rs1884589	0.87[EUR][1000 genomes]
rs1884590	0.87[EUR][1000 genomes]
rs1884595	0.84[EUR][1000 genomes]
rs1980571	0.87[EUR][1000 genomes]
rs1986765	0.83[EUR][1000 genomes]
rs1987488	0.85[EUR][1000 genomes]
rs1988545	0.83[EUR][1000 genomes]
rs1998076	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2009652	0.81[EUR][1000 genomes]
rs2010733	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201547	0.82[EUR][1000 genomes]
rs201548	0.81[EUR][1000 genomes]
rs2016964	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024885	0.83[EUR][1000 genomes]
rs2180438	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180439	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2208050	0.83[EUR][1000 genomes]
rs2208051	0.82[EUR][1000 genomes]
rs2208052	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208054	0.85[EUR][1000 genomes]
rs2208055	0.85[EUR][1000 genomes]
rs2224261	0.92[ASN][1000 genomes]
rs2254540	0.83[EUR][1000 genomes]
rs2281526	0.83[EUR][1000 genomes]
rs2328678	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328679	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328680	0.83[EUR][1000 genomes]
rs2328681	0.83[EUR][1000 genomes]
rs2328682	0.83[EUR][1000 genomes]
rs2328684	0.83[EUR][1000 genomes]
rs2424418	0.83[EUR][1000 genomes]
rs2424419	0.83[EUR][1000 genomes]
rs2424421	0.82[EUR][1000 genomes]
rs2424423	0.82[EUR][1000 genomes]
rs2876614	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818179	0.84[EUR][1000 genomes]
rs3818180	0.84[EUR][1000 genomes]
rs3818181	0.84[EUR][1000 genomes]
rs3818182	0.84[EUR][1000 genomes]
rs3818183	0.84[EUR][1000 genomes]
rs4390829	0.85[EUR][1000 genomes]
rs4405823	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544515	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4815071	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815072	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815073	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4815076	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4815080	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4815081	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4815082	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6035961	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6035968	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6035969	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6035970	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6035980	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6035982	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6036003	0.82[EUR][1000 genomes]
rs6036007	0.81[EUR][1000 genomes]
rs6047658	0.92[ASN][1000 genomes]
rs6047660	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6047661	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6047662	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6047663	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6047676	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047677	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6047679	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047681	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047682	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047683	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047684	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047691	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047692	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047694	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6047705	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6047709	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6047713	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6047714	0.86[EUR][1000 genomes]
rs6047715	0.86[EUR][1000 genomes]
rs6047731	0.85[EUR][1000 genomes]
rs6047732	0.85[EUR][1000 genomes]
rs6047733	0.85[EUR][1000 genomes]
rs6047743	0.83[EUR][1000 genomes]
rs6047744	0.83[EUR][1000 genomes]
rs6047745	0.83[EUR][1000 genomes]
rs6047749	0.82[EUR][1000 genomes]
rs6047768	0.83[EUR][1000 genomes]
rs6047769	0.82[EUR][1000 genomes]
rs6075842	0.88[ASN][1000 genomes]
rs6075843	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6075852	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6075853	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6075854	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6075855	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6075858	0.85[EUR][1000 genomes]
rs6075861	0.82[EUR][1000 genomes]
rs6082520	0.88[ASN][1000 genomes]
rs6082524	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082525	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6082533	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6082540	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6082541	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6082544	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6082553	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6082556	0.87[EUR][1000 genomes]
rs6082560	0.84[EUR][1000 genomes]
rs6106421	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106438	0.81[EUR][1000 genomes]
rs6113393	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6113394	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6113395	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6113404	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6113413	0.88[EUR][1000 genomes]
rs6113414	0.88[EUR][1000 genomes]
rs6113415	0.86[EUR][1000 genomes]
rs6113416	0.87[EUR][1000 genomes]
rs6113418	0.87[EUR][1000 genomes]
rs6113424	0.83[EUR][1000 genomes]
rs6113425	0.83[EUR][1000 genomes]
rs6113431	0.83[EUR][1000 genomes]
rs6113435	0.83[EUR][1000 genomes]
rs6137473	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6137476	0.84[EUR][1000 genomes]
rs6515191	0.83[EUR][1000 genomes]
rs718664	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7261950	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs761890	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs761891	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs764777	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8116929	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121238	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8122229	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs927059	0.81[EUR][1000 genomes]
rs932540	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs966604	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs987050	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997078	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv912814	chr20:21703615-21946928	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13039748	PAX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:21818800-21820800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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