Variant report

Variant	rs7827446
Chromosome Location	chr8:52233408-52233409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNTG1-1	chr8:52233280-52233678	ENSG00000253664.1

Extended variants
information (count: 164 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1003095	0.95[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10091279	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs10092020	0.81[EUR][1000 genomes]
rs10094879	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10097749	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10101803	0.95[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs10102454	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10105228	0.99[EUR][1000 genomes]
rs10107148	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10110193	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113485	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1017352	0.95[CEU][hapmap]
rs1017353	0.95[CEU][hapmap]
rs1017354	0.95[CEU][hapmap]
rs1052704	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10958261	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11989863	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11991037	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11993179	0.83[EUR][1000 genomes]
rs1219677	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1219680	0.95[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1236097	0.95[CEU][hapmap]
rs12542121	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12543420	0.81[ASN][1000 genomes]
rs12549831	0.85[ASN][1000 genomes]
rs12550267	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1346954	0.95[CEU][hapmap]
rs1370443	0.82[ASN][1000 genomes]
rs1370444	0.82[ASN][1000 genomes]
rs1370445	0.84[CEU][hapmap];0.89[MEX][hapmap]
rs1370446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431619	0.95[CEU][hapmap];0.84[GIH][hapmap]
rs1431620	0.95[CEU][hapmap]
rs1431623	0.94[CEU][hapmap]
rs1431624	0.94[CEU][hapmap]
rs1431625	0.95[CEU][hapmap]
rs1431626	0.95[CEU][hapmap]
rs1431627	0.95[CEU][hapmap]
rs1431628	0.95[CEU][hapmap]
rs1560508	0.95[CEU][hapmap]
rs1560509	0.95[CEU][hapmap]
rs1560510	0.95[CEU][hapmap]
rs16915954	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16915972	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16916011	0.80[EUR][1000 genomes]
rs17261657	0.89[CEU][hapmap]
rs1816630	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1837086	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837087	0.99[EUR][1000 genomes]
rs1991691	0.95[CEU][hapmap]
rs1991692	0.95[CEU][hapmap]
rs2217988	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28417640	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28449829	0.99[EUR][1000 genomes]
rs28522270	0.80[EUR][1000 genomes]
rs28534083	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28805429	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2915454	0.95[CEU][hapmap]
rs2915457	0.95[CEU][hapmap]
rs2915460	0.95[CEU][hapmap]
rs2915461	0.95[CEU][hapmap]
rs2915465	0.95[CEU][hapmap]
rs2915467	0.94[CEU][hapmap]
rs2915468	0.95[CEU][hapmap]
rs2915469	0.95[CEU][hapmap]
rs2915471	0.94[CEU][hapmap]
rs2915473	0.95[CEU][hapmap]
rs2915475	0.95[CEU][hapmap]
rs2915476	0.95[CEU][hapmap]
rs2915477	0.95[CEU][hapmap]
rs2915479	0.94[CEU][hapmap]
rs2915480	0.95[CEU][hapmap]
rs2915481	0.95[CEU][hapmap]
rs2915482	0.95[CEU][hapmap]
rs2915483	0.95[CEU][hapmap]
rs2915484	0.95[CEU][hapmap]
rs2915485	0.95[CEU][hapmap]
rs2915489	0.84[CEU][hapmap]
rs2976984	0.95[CEU][hapmap]
rs2976985	0.95[CEU][hapmap]
rs2976986	0.95[CEU][hapmap]
rs2976988	0.95[CEU][hapmap]
rs2976989	0.95[CEU][hapmap]
rs2976990	0.95[CEU][hapmap]
rs2976991	0.95[CEU][hapmap]
rs2976992	0.94[CEU][hapmap]
rs2976993	0.95[CEU][hapmap]
rs2976994	0.94[CEU][hapmap]
rs3097703	0.95[CEU][hapmap]
rs3097704	0.95[CEU][hapmap]
rs3097705	0.95[CEU][hapmap]
rs3097706	0.95[CEU][hapmap]
rs3115784	0.95[CEU][hapmap]
rs35426341	0.85[ASN][1000 genomes]
rs4471026	0.85[EUR][1000 genomes]
rs4500070	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs4873189	0.80[CEU][hapmap]
rs4873190	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4873192	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873530	0.85[CEU][hapmap]
rs4873533	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4873534	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4873540	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873541	0.82[EUR][1000 genomes]
rs4873542	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873543	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4873544	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4873545	0.81[EUR][1000 genomes]
rs57224283	0.82[ASN][1000 genomes]
rs60579236	0.83[EUR][1000 genomes]
rs60646659	0.81[EUR][1000 genomes]
rs6473594	0.82[EUR][1000 genomes]
rs6473595	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66555193	0.99[EUR][1000 genomes]
rs67110071	0.83[EUR][1000 genomes]
rs67134977	0.81[EUR][1000 genomes]
rs67152383	0.83[EUR][1000 genomes]
rs6981422	0.81[EUR][1000 genomes]
rs6986651	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6987616	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6987775	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6992933	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6996951	0.95[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs6998723	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6998855	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6999446	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7000176	0.81[EUR][1000 genomes]
rs7003720	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7004460	0.82[EUR][1000 genomes]
rs7008365	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7016124	0.88[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7016775	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7017403	1.00[CEU][hapmap];0.86[JPT][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7017421	1.00[CEU][hapmap];0.86[JPT][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs726127	0.81[EUR][1000 genomes]
rs766788	0.95[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs766789	0.81[EUR][1000 genomes]
rs766790	0.95[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs7813377	0.82[EUR][1000 genomes]
rs7814566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7817771	0.81[EUR][1000 genomes]
rs7818411	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7818590	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7818710	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7821565	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7825017	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7827306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828080	0.82[EUR][1000 genomes]
rs7834299	0.82[EUR][1000 genomes]
rs7839630	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7840437	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs7842457	0.99[EUR][1000 genomes]
rs7844531	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7844947	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7845311	0.83[EUR][1000 genomes]
rs7846115	0.81[EUR][1000 genomes]
rs9298442	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9298443	0.82[EUR][1000 genomes]
rs9298444	0.95[CEU][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs972025	0.95[CEU][hapmap]
rs972026	0.95[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932026	chr8:51858658-52758574	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948338	chr8:52060314-52368754	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv890895	chr8:52190571-52615191	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7827446	RDM1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:52221200-52238000	Weak transcription	Left Ventricle	heart

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