Variant report

Variant	rs6515535
Chromosome Location	chr20:24823962-24823963
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	chr20:24820307..24822750-chr20:24822757..24824794,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1029032	0.81[EUR][1000 genomes]
rs11087480	0.91[EUR][1000 genomes]
rs11700139	1.00[ASN][1000 genomes]
rs11700161	1.00[ASN][1000 genomes]
rs11906401	0.91[EUR][1000 genomes]
rs11906511	0.92[EUR][1000 genomes]
rs1571772	1.00[ASN][1000 genomes]
rs2064404	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap]
rs2150644	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239751	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap]
rs4815358	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs4815359	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs55681373	0.83[EUR][1000 genomes]
rs55905952	1.00[ASN][1000 genomes]
rs55979003	1.00[ASN][1000 genomes]
rs56000345	1.00[ASN][1000 genomes]
rs56053259	0.86[EUR][1000 genomes]
rs56148678	0.92[EUR][1000 genomes]
rs56249107	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56299926	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56406017	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58353086	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036939	0.91[EUR][1000 genomes]
rs6036940	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036948	0.88[EUR][1000 genomes]
rs6049996	1.00[ASN][1000 genomes]
rs6050002	1.00[ASN][1000 genomes]
rs6050026	0.92[EUR][1000 genomes]
rs6050052	0.91[EUR][1000 genomes]
rs6050056	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6050066	0.88[EUR][1000 genomes]
rs6050123	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6050199	0.83[CEU][hapmap];0.90[YRI][hapmap]
rs6076279	1.00[ASN][1000 genomes]
rs6076281	1.00[ASN][1000 genomes]
rs6076283	1.00[ASN][1000 genomes]
rs6076288	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076289	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076291	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076293	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083630	1.00[ASN][1000 genomes]
rs6083632	1.00[ASN][1000 genomes]
rs6083633	1.00[ASN][1000 genomes]
rs6083638	0.91[EUR][1000 genomes]
rs6083639	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083645	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083646	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083647	0.91[EUR][1000 genomes]
rs6083649	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6083650	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083651	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083653	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083657	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083697	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap]
rs6083714	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap]
rs6106957	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6106965	1.00[ASN][1000 genomes]
rs6106967	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114893	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62215819	1.00[ASN][1000 genomes]
rs62215821	1.00[ASN][1000 genomes]
rs62215822	1.00[ASN][1000 genomes]
rs62215823	1.00[ASN][1000 genomes]
rs62215824	1.00[ASN][1000 genomes]
rs62215826	1.00[ASN][1000 genomes]
rs7262604	1.00[ASN][1000 genomes]
rs7269852	1.00[ASN][1000 genomes]
rs73101427	1.00[ASN][1000 genomes]
rs73108128	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110258	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73110260	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337207	1.00[ASN][1000 genomes]
rs7509561	1.00[ASN][1000 genomes]
rs761368	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs765834	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs8114708	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114760	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8117102	1.00[ASN][1000 genomes]
rs8117164	1.00[ASN][1000 genomes]
rs8119191	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8120506	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8123541	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914308	0.92[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
rs6515535	C20orf191	cis	cerebellum	SCAN
rs6515535	C20orf3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24822600-24824400	Enhancers	Primary hematopoietic stem cells	blood
2	chr20:24822800-24824200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:24822800-24824200	Enhancers	Primary B cells from peripheral blood	blood
4	chr20:24823000-24824000	Enhancers	Primary B cells from cord blood	blood
5	chr20:24823000-24824200	Enhancers	Adipose Nuclei	Adipose
6	chr20:24823000-24824200	Flanking Active TSS	GM12878-XiMat	blood
7	chr20:24823200-24824200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr20:24823400-24824000	Active TSS	Duodenum Mucosa	Duodenum
9	chr20:24823400-24824200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr20:24823400-24824200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr20:24823600-24824000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr20:24823800-24824000	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr20:24823800-24824000	Enhancers	Fetal Lung	lung
14	chr20:24823800-24824200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr20:24823800-24824600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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