Variant report

Variant	rs6083647
Chromosome Location	chr20:24840615-24840616
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1029031	1.00[ASN][1000 genomes]
rs1029032	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029033	1.00[ASN][1000 genomes]
rs11087480	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1113872	1.00[ASN][1000 genomes]
rs1122607	1.00[ASN][1000 genomes]
rs11905160	1.00[ASN][1000 genomes]
rs11906401	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11906511	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331285	1.00[ASN][1000 genomes]
rs1331290	1.00[ASN][1000 genomes]
rs1411892	1.00[ASN][1000 genomes]
rs1411894	1.00[ASN][1000 genomes]
rs1411895	1.00[ASN][1000 genomes]
rs1831483	1.00[ASN][1000 genomes]
rs1888655	1.00[ASN][1000 genomes]
rs2064404	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap]
rs2150644	0.83[EUR][1000 genomes]
rs4239751	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap]
rs4815358	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs4815359	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs55702326	1.00[ASN][1000 genomes]
rs56053259	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56106395	1.00[ASN][1000 genomes]
rs56148678	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56179484	1.00[ASN][1000 genomes]
rs56249107	0.90[EUR][1000 genomes]
rs56299926	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56406017	0.86[EUR][1000 genomes]
rs58353086	0.93[EUR][1000 genomes]
rs6036915	1.00[ASN][1000 genomes]
rs6036939	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036940	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036943	1.00[ASN][1000 genomes]
rs6036946	1.00[ASN][1000 genomes]
rs6036948	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036951	1.00[ASN][1000 genomes]
rs6036955	1.00[ASN][1000 genomes]
rs6036967	1.00[ASN][1000 genomes]
rs6036968	1.00[ASN][1000 genomes]
rs6036969	1.00[ASN][1000 genomes]
rs6036970	1.00[ASN][1000 genomes]
rs6036971	1.00[ASN][1000 genomes]
rs6036972	1.00[ASN][1000 genomes]
rs6050000	1.00[ASN][1000 genomes]
rs6050007	1.00[ASN][1000 genomes]
rs6050026	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050051	1.00[ASN][1000 genomes]
rs6050052	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050056	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050058	1.00[ASN][1000 genomes]
rs6050066	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050070	1.00[ASN][1000 genomes]
rs6050073	1.00[ASN][1000 genomes]
rs6050074	1.00[ASN][1000 genomes]
rs6050111	1.00[ASN][1000 genomes]
rs6050114	1.00[ASN][1000 genomes]
rs6050115	1.00[ASN][1000 genomes]
rs6050116	1.00[ASN][1000 genomes]
rs6050117	1.00[ASN][1000 genomes]
rs6050119	1.00[ASN][1000 genomes]
rs6050120	1.00[ASN][1000 genomes]
rs6050121	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6050123	0.84[AMR][1000 genomes]
rs6050124	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6050199	0.83[CEU][hapmap]
rs6076288	0.92[EUR][1000 genomes]
rs6076289	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6076290	1.00[ASN][1000 genomes]
rs6076291	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6076292	1.00[ASN][1000 genomes]
rs6076293	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6083628	1.00[ASN][1000 genomes]
rs6083638	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083639	0.90[EUR][1000 genomes]
rs6083645	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6083646	0.93[EUR][1000 genomes]
rs6083648	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083649	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083650	0.91[EUR][1000 genomes]
rs6083651	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6083653	0.90[EUR][1000 genomes]
rs6083656	1.00[ASN][1000 genomes]
rs6083657	0.90[EUR][1000 genomes]
rs6083658	1.00[ASN][1000 genomes]
rs6083697	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap]
rs6083714	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs6106957	0.93[EUR][1000 genomes]
rs6106963	1.00[ASN][1000 genomes]
rs6106967	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6106968	1.00[ASN][1000 genomes]
rs6114893	0.93[EUR][1000 genomes]
rs6114915	1.00[ASN][1000 genomes]
rs6114918	1.00[ASN][1000 genomes]
rs6114921	1.00[ASN][1000 genomes]
rs62215832	1.00[ASN][1000 genomes]
rs6515535	0.91[EUR][1000 genomes]
rs6515538	1.00[ASN][1000 genomes]
rs73108128	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73110258	0.81[EUR][1000 genomes]
rs73110260	0.82[EUR][1000 genomes]
rs761368	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs765834	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs8114708	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8114760	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8119191	0.92[EUR][1000 genomes]
rs8120506	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8123541	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs914308	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914309	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1061455	chr20:24733120-24861801	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544218	chr20:24733120-24861801	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6083647	C20orf3	cis	parietal	SCAN
rs6083647	C20orf191	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24837600-24841200	ZNF genes & repeats	Dnd41	blood
2	chr20:24839200-24840800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr20:24839400-24840800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr20:24840400-24840800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived

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