Variant report

Variant	rs7269852
Chromosome Location	chr20:24797175-24797176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1122607	0.85[EUR][1000 genomes]
rs11697463	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11700139	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700161	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1413069	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1571772	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888655	0.82[EUR][1000 genomes]
rs2064404	1.00[CHB][hapmap]
rs2150644	1.00[ASN][1000 genomes]
rs4239751	1.00[CHB][hapmap]
rs4815358	1.00[CHB][hapmap]
rs4815359	1.00[CHB][hapmap]
rs55905952	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55979003	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56000345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56249107	1.00[ASN][1000 genomes]
rs56299926	1.00[ASN][1000 genomes]
rs56406017	1.00[ASN][1000 genomes]
rs58353086	1.00[ASN][1000 genomes]
rs6036915	0.86[EUR][1000 genomes]
rs6036940	1.00[ASN][1000 genomes]
rs6036943	0.81[EUR][1000 genomes]
rs6036946	0.81[EUR][1000 genomes]
rs6049996	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050000	0.86[EUR][1000 genomes]
rs6050002	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050007	0.83[EUR][1000 genomes]
rs6050058	0.81[EUR][1000 genomes]
rs6076279	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076281	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076283	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076288	1.00[ASN][1000 genomes]
rs6076289	1.00[ASN][1000 genomes]
rs6076290	0.81[EUR][1000 genomes]
rs6076291	1.00[ASN][1000 genomes]
rs6076293	1.00[ASN][1000 genomes]
rs6083628	0.90[EUR][1000 genomes]
rs6083630	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083631	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6083632	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083633	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083639	1.00[ASN][1000 genomes]
rs6083645	1.00[ASN][1000 genomes]
rs6083646	1.00[ASN][1000 genomes]
rs6083650	1.00[ASN][1000 genomes]
rs6083651	1.00[ASN][1000 genomes]
rs6083653	1.00[ASN][1000 genomes]
rs6083657	1.00[ASN][1000 genomes]
rs6083697	1.00[CHB][hapmap]
rs6083714	1.00[CHB][hapmap]
rs6106957	1.00[ASN][1000 genomes]
rs6106965	1.00[ASN][1000 genomes]
rs6106967	1.00[ASN][1000 genomes]
rs62215817	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62215819	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215820	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62215821	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215822	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215823	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215824	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215826	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515535	1.00[ASN][1000 genomes]
rs6515538	0.82[EUR][1000 genomes]
rs7262604	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73101427	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73108128	1.00[ASN][1000 genomes]
rs73110258	1.00[ASN][1000 genomes]
rs73110260	1.00[ASN][1000 genomes]
rs73337207	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7509561	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761368	1.00[CHB][hapmap]
rs765834	1.00[CHB][hapmap]
rs8114708	1.00[ASN][1000 genomes]
rs8114760	1.00[ASN][1000 genomes]
rs8117102	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8117164	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8119191	1.00[ASN][1000 genomes]
rs8120506	1.00[ASN][1000 genomes]
rs8123541	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7269852	C20orf3	cis	parietal	SCAN

Chromatin state (count:4 , 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	chr20:24796600-24797600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:24796600-24798800	Enhancers	Spleen	Spleen
4	chr20:24797000-24798600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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