Variant report

Variant	rs6050118
Chromosome Location	chr20:24891895-24891896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1007881	0.86[JPT][hapmap]
rs1056036	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11087486	0.82[ASN][1000 genomes]
rs11700073	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11905625	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1331286	0.90[ASN][1000 genomes]
rs1535042	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1854849	0.90[ASN][1000 genomes]
rs1977540	0.88[ASN][1000 genomes]
rs2008275	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2179732	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2235847	0.85[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs227619	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227620	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227623	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227625	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs227626	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227628	0.81[ASN][1000 genomes]
rs227633	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227634	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227635	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227639	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227643	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227646	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227648	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227652	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227653	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227657	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs227659	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2387365	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3746330	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4273288	0.88[ASN][1000 genomes]
rs4539860	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs45468392	0.81[ASN][1000 genomes]
rs45556041	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4594518	0.86[ASN][1000 genomes]
rs4815327	0.88[ASN][1000 genomes]
rs4815351	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4815357	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6036976	0.88[ASN][1000 genomes]
rs6050131	0.86[ASN][1000 genomes]
rs6050134	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6050198	0.85[CHB][hapmap]
rs6050201	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6050249	0.82[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6050255	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050259	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6050261	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6083699	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6083709	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6114980	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6114981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6114984	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6132775	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6132777	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6132778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6132783	0.80[AMR][1000 genomes]
rs6132784	0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6132789	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6138396	0.87[ASN][1000 genomes]
rs6138406	0.86[ASN][1000 genomes]
rs6138437	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6138438	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6138442	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6138453	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6138455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6138457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6138458	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6138460	0.80[AMR][1000 genomes]
rs6138466	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6138473	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6138474	0.86[JPT][hapmap]
rs6138475	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs62215110	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62215115	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62215128	0.80[AMR][1000 genomes]
rs62215131	0.80[AMR][1000 genomes]
rs6707	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7268095	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8125909	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs8183891	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs914314	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv432115	chr20:24871385-24915839	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058559	chr20:24880415-24923818	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1061536	chr20:24880777-24930642	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1060158	chr20:24887819-24918081	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1066090	chr20:24887819-24923818	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1065568	chr20:24887819-24925706	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6050118	CST7	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24891400-24893600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24891800-24892200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr20:24891800-24892600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr20:24891800-24896000	Weak transcription	Spleen	Spleen

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