Variant report

Variant	rs2396893
Chromosome Location	chr6:48957329-48957330
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1018375	0.82[EUR][1000 genomes]
rs1018376	0.82[EUR][1000 genomes]
rs1018377	0.82[EUR][1000 genomes]
rs10456135	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456136	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456137	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10456138	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456139	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10456599	0.82[EUR][1000 genomes]
rs10456600	0.82[EUR][1000 genomes]
rs10456602	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456603	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456604	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456605	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456608	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10456609	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10456610	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10456611	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10456615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10484428	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10948454	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10948456	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10948457	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10948458	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10948459	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10948460	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10948461	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10948462	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10948467	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11752248	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11754375	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11759121	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12189600	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12189939	0.83[EUR][1000 genomes]
rs12191149	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12191723	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12191941	0.84[AMR][1000 genomes]
rs12192567	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12194532	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12195722	0.80[EUR][1000 genomes]
rs12195778	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12196951	0.83[AMR][1000 genomes]
rs12197769	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12197814	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12197837	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12197864	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12198032	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12198713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12199196	0.83[EUR][1000 genomes]
rs12199437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12199643	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12199804	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12200106	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12200323	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12202633	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12204534	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12204983	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12205727	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12205825	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12206241	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12206784	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12207012	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12207213	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12208940	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12209021	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12209068	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12210033	0.82[EUR][1000 genomes]
rs12213551	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12213614	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12213753	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12215635	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12216136	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12216234	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13204786	0.82[AMR][1000 genomes]
rs17574427	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17574802	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1938199	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1938217	0.81[EUR][1000 genomes]
rs1938219	0.82[EUR][1000 genomes]
rs1938221	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1938222	0.82[EUR][1000 genomes]
rs1938223	0.82[EUR][1000 genomes]
rs1984868	0.83[EUR][1000 genomes]
rs2049962	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2179180	0.88[AMR][1000 genomes]
rs2179181	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2205868	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2205871	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2396889	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2396890	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2894756	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2894757	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35014712	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35059425	0.84[AMR][1000 genomes]
rs35340842	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4364469	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4425594	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4489145	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711921	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4711922	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4711923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715112	0.83[EUR][1000 genomes]
rs4715113	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4715115	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4715118	0.88[AMR][1000 genomes]
rs62412793	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62412794	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62413171	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6903814	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906485	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6931724	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6940005	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7742341	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7742500	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7744578	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7753035	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756535	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7759998	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7764697	0.81[EUR][1000 genomes]
rs7771350	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7771351	0.82[EUR][1000 genomes]
rs9395433	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs990710	0.89[AMR][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	nsv949690	chr6:48595821-49289855	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv603037	chr6:48804862-48995221	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv603049	chr6:48931959-49169337	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:48951200-48957400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:48957000-48958600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:48957000-48962400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:48957200-48957800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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