Variant report

Variant	rs2260966
Chromosome Location	chr6:63102796-63102797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10945156	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10945189	0.83[EUR][1000 genomes]
rs10945226	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758619	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12528424	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12660844	0.83[EUR][1000 genomes]
rs12662273	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12663464	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16882876	0.80[EUR][1000 genomes]
rs16883133	0.83[EUR][1000 genomes]
rs16884023	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16884157	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16884169	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1688991	0.83[EUR][1000 genomes]
rs1855604	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2345330	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2345331	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2492796	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2492802	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2495266	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2495267	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2639412	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2639413	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2639414	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2639415	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2639419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639446	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2639447	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2639448	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2639450	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2679573	0.80[EUR][1000 genomes]
rs2814648	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814649	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814650	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814651	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2814652	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814654	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814655	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2814658	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2814659	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2814660	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2814678	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2814680	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814681	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2842798	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842799	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842802	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2842809	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2842810	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2842812	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs486719	0.80[EUR][1000 genomes]
rs494833	0.83[EUR][1000 genomes]
rs516904	0.83[EUR][1000 genomes]
rs524169	0.83[EUR][1000 genomes]
rs549603	0.80[EUR][1000 genomes]
rs573454	0.80[EUR][1000 genomes]
rs581435	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs590059	0.83[EUR][1000 genomes]
rs591353	0.83[EUR][1000 genomes]
rs591366	0.83[EUR][1000 genomes]
rs603987	0.83[EUR][1000 genomes]
rs606199	0.83[EUR][1000 genomes]
rs62414796	0.80[EUR][1000 genomes]
rs62414811	0.83[EUR][1000 genomes]
rs62416568	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62416569	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62416570	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62416571	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62416572	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs627630	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs630414	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs646854	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs675484	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs677360	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6908177	0.80[EUR][1000 genomes]
rs6918262	0.83[EUR][1000 genomes]
rs6934952	0.80[EUR][1000 genomes]
rs73488982	0.80[EUR][1000 genomes]
rs7742126	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7743214	0.83[EUR][1000 genomes]
rs7750698	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7770793	0.80[EUR][1000 genomes]
rs7772645	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs855409	0.80[EUR][1000 genomes]
rs855412	0.80[EUR][1000 genomes]
rs855413	0.80[EUR][1000 genomes]
rs855414	0.80[EUR][1000 genomes]
rs876854	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9294829	0.80[EUR][1000 genomes]
rs9294844	0.83[EUR][1000 genomes]
rs9446139	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9446154	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs9454804	0.80[EUR][1000 genomes]
rs9454831	0.83[EUR][1000 genomes]
rs9454832	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9454834	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9454844	0.83[EUR][1000 genomes]
rs9454845	0.83[EUR][1000 genomes]
rs9454859	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes]
rs9918343	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017249	chr6:62906813-63317382	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1020677	chr6:62911584-63309663	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv532025	chr6:62944349-63571677	Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv916760	chr6:62944661-63290986	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1029503	chr6:63033365-63698355	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv603350	chr6:63066240-63152724	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
7	nsv462967	chr6:63069063-63173293	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv603351	chr6:63069063-63173293	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv532026	chr6:63085396-63698477	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv917014	chr6:63085410-63698365	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2260966	CDC26	trans	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:63100800-63103600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:63102000-63105000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:63102400-63103400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:63102400-63104400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:63102600-63103600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:63102600-63104200	Enhancers	HUES48 Cell Line	embryonic stem cell

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