Variant report

Variant	rs6083628
Chromosome Location	chr20:24798856-24798857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24797658..24800025-chr20:24806940..24809429,2	MCF-7	breast:

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1029031	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1029032	1.00[ASN][1000 genomes]
rs1029033	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11087480	1.00[ASN][1000 genomes]
rs1113872	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1122607	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11697463	0.90[EUR][1000 genomes]
rs11700139	0.90[EUR][1000 genomes]
rs11700161	0.90[EUR][1000 genomes]
rs11905160	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11906401	1.00[ASN][1000 genomes]
rs11906511	1.00[ASN][1000 genomes]
rs1331285	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1331290	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411892	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411894	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411895	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413069	0.89[EUR][1000 genomes]
rs1571772	0.90[EUR][1000 genomes]
rs1831483	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888655	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008275	0.87[ASW][hapmap];0.90[LWK][hapmap]
rs2064404	1.00[CHB][hapmap]
rs2235847	0.87[ASW][hapmap];0.87[LWK][hapmap]
rs35326290	0.94[AFR][1000 genomes]
rs4239751	1.00[CHB][hapmap]
rs4815358	1.00[CHB][hapmap]
rs4815359	1.00[CHB][hapmap]
rs55702326	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55905952	0.88[EUR][1000 genomes]
rs55979003	0.88[EUR][1000 genomes]
rs56000345	0.91[EUR][1000 genomes]
rs56053259	1.00[ASN][1000 genomes]
rs56106395	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56148678	1.00[ASN][1000 genomes]
rs56179484	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036915	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036939	1.00[ASN][1000 genomes]
rs6036943	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036946	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036948	1.00[ASN][1000 genomes]
rs6036951	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036955	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036967	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036968	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036969	1.00[ASN][1000 genomes]
rs6036970	1.00[ASN][1000 genomes]
rs6036971	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036972	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049996	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6050000	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050002	0.89[EUR][1000 genomes]
rs6050007	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050026	1.00[ASN][1000 genomes]
rs6050051	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050052	1.00[ASN][1000 genomes]
rs6050056	1.00[ASN][1000 genomes]
rs6050058	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050066	1.00[ASN][1000 genomes]
rs6050070	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050073	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050074	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050111	1.00[ASN][1000 genomes]
rs6050114	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050115	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050116	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050117	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050119	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050120	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076279	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6076281	0.89[EUR][1000 genomes]
rs6076283	0.89[EUR][1000 genomes]
rs6076290	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076292	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083630	0.91[EUR][1000 genomes]
rs6083631	0.89[EUR][1000 genomes]
rs6083632	0.89[EUR][1000 genomes]
rs6083633	0.88[EUR][1000 genomes]
rs6083638	1.00[ASN][1000 genomes]
rs6083647	1.00[ASN][1000 genomes]
rs6083648	1.00[ASN][1000 genomes]
rs6083649	1.00[ASN][1000 genomes]
rs6083652	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6083656	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083658	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083697	1.00[CHB][hapmap]
rs6083714	1.00[CHB][hapmap]
rs6106963	1.00[ASN][1000 genomes]
rs6106968	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106969	0.80[EUR][1000 genomes]
rs6114915	1.00[ASN][1000 genomes]
rs6114918	1.00[ASN][1000 genomes]
rs6114921	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138396	0.82[AFR][1000 genomes]
rs62215817	0.89[EUR][1000 genomes]
rs62215819	0.91[EUR][1000 genomes]
rs62215820	0.90[EUR][1000 genomes]
rs62215821	0.90[EUR][1000 genomes]
rs62215822	0.91[EUR][1000 genomes]
rs62215823	0.91[EUR][1000 genomes]
rs62215824	0.89[EUR][1000 genomes]
rs62215826	0.89[EUR][1000 genomes]
rs62215832	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515538	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7262604	0.88[EUR][1000 genomes]
rs7269852	0.90[EUR][1000 genomes]
rs73101427	0.90[EUR][1000 genomes]
rs73337207	0.90[EUR][1000 genomes]
rs7509561	0.90[EUR][1000 genomes]
rs761368	1.00[CHB][hapmap]
rs765834	1.00[CHB][hapmap]
rs8117102	0.88[EUR][1000 genomes]
rs8117164	0.88[EUR][1000 genomes]
rs914308	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1061281	chr20:24711635-24815107	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv544217	chr20:24711635-24815107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv912825	chr20:24715544-24813345	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6083628	C20orf191	cis	cerebellum	SCAN
rs6083628	GGTLC1	cis	parietal	SCAN
rs6083628	C20orf3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24794200-24817600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24798800-24799800	Weak transcription	Spleen	Spleen

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