Variant report

Variant	rs675484
Chromosome Location	chr6:63154495-63154496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10945189	0.81[EUR][1000 genomes]
rs10945226	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11758619	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12528424	0.90[EUR][1000 genomes]
rs12660844	0.81[EUR][1000 genomes]
rs12662273	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12663464	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16883133	0.81[EUR][1000 genomes]
rs16884023	0.90[EUR][1000 genomes]
rs16884169	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1688991	0.81[EUR][1000 genomes]
rs1855604	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2260966	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2345330	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2345331	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2492796	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2492802	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2495266	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2495267	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2639412	0.90[EUR][1000 genomes]
rs2639413	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2639414	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2639415	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2639419	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2639446	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2639447	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2639448	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2639450	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2814648	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814649	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814650	0.90[EUR][1000 genomes]
rs2814651	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814652	0.90[EUR][1000 genomes]
rs2814654	0.90[EUR][1000 genomes]
rs2814655	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814658	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2814659	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2814660	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2814678	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2814680	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2814681	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2842798	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2842799	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2842802	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2842809	0.90[EUR][1000 genomes]
rs2842810	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2842812	0.90[EUR][1000 genomes]
rs494833	0.81[EUR][1000 genomes]
rs516904	0.81[EUR][1000 genomes]
rs524169	0.81[EUR][1000 genomes]
rs581435	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs590059	0.81[EUR][1000 genomes]
rs591353	0.81[EUR][1000 genomes]
rs591366	0.81[EUR][1000 genomes]
rs603987	0.81[EUR][1000 genomes]
rs606199	0.81[EUR][1000 genomes]
rs62414811	0.81[EUR][1000 genomes]
rs62416568	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62416569	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62416570	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62416571	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62416572	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs627630	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630414	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs646854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6918262	0.81[EUR][1000 genomes]
rs7743214	0.81[EUR][1000 genomes]
rs7750698	0.81[EUR][1000 genomes]
rs7772645	0.81[EUR][1000 genomes]
rs876854	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9294844	0.81[EUR][1000 genomes]
rs9446139	0.81[EUR][1000 genomes]
rs9446154	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs9454831	0.81[EUR][1000 genomes]
rs9454832	0.81[EUR][1000 genomes]
rs9454834	0.81[EUR][1000 genomes]
rs9454844	0.81[EUR][1000 genomes]
rs9454845	0.81[EUR][1000 genomes]
rs9454859	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
7	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
8	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
9	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
10	nsv1030631	chr6:63111798-63225697	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv9893	chr6:63141271-63155169	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
12	nsv885967	chr6:63152724-63605221	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs675484	CDC26	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:63151400-63155400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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