Variant report

Variant	rs6135530
Chromosome Location	chr20:15777250-15777251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12624706	0.82[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs13039564	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13041254	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13042688	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13044785	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16996587	0.94[CEU][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1997798	0.89[EUR][1000 genomes]
rs2109535	0.84[EUR][1000 genomes]
rs2109536	0.89[EUR][1000 genomes]
rs2327966	1.00[CEU][hapmap]
rs33952091	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35973686	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36034970	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4292145	0.87[EUR][1000 genomes]
rs4426588	0.87[EUR][1000 genomes]
rs4627651	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4813196	0.85[GIH][hapmap];0.85[TSI][hapmap]
rs6043539	0.82[CEU][hapmap]
rs6131706	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6131713	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6131714	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6131715	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6131716	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6131717	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6131718	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6131727	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6135506	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6135508	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6135509	0.83[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6135511	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs6135512	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6135514	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6135519	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6135520	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6135521	0.84[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6135528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135531	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6135543	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6135545	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6135557	0.81[GIH][hapmap]
rs62194716	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6514613	0.87[CEU][hapmap]
rs7269144	0.94[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7273944	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs761262	0.94[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs764140	0.82[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs877270	0.94[CEU][hapmap]
rs877271	0.94[CEU][hapmap]
rs979530	0.89[EUR][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	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv833928	chr20:15619962-15780758	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv519883	chr20:15738086-15817106	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv585643	chr20:15759361-15796051	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv912793	chr20:15760969-15807441	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv833929	chr20:15765372-15977337	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1847965	chr20:15766727-15807441	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv585644	chr20:15766727-15807441	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6135530	POLR3F	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15770800-15780000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr20:15773600-15777600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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