Variant report

Variant	rs1339258
Chromosome Location	chr20:15956742-15956743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1012298	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs12624676	0.83[ASN][1000 genomes]
rs1339257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281418	0.83[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs6034328	0.85[CHB][hapmap]
rs6043620	0.85[CHB][hapmap]
rs6074979	0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6074980	0.83[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6074983	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6074984	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6080023	0.85[CHB][hapmap]
rs6080044	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs6080048	0.83[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs6080050	0.83[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs6080052	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6080055	0.95[ASN][1000 genomes]
rs6080056	0.95[ASN][1000 genomes]
rs6080057	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs6080058	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs6080064	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6080069	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6105492	0.81[CHD][hapmap]
rs6105504	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6110832	0.89[CHB][hapmap]
rs6110847	0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6110848	0.89[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs6131738	0.80[CHB][hapmap]
rs6131743	0.81[ASN][1000 genomes]
rs6131745	0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs6131747	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs6131748	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6131749	0.83[ASN][1000 genomes]
rs6131750	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6135602	0.82[CHD][hapmap]
rs6135608	0.85[CHD][hapmap]
rs6135620	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6135621	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6135622	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs766970	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	esv3447866	chr20:15799286-16115291	Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1339258	POLR3F	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15953000-15959800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr20:15953400-15957400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:15954600-15959200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr20:15954800-15958800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr20:15955000-15957800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:15955400-15957000	Weak transcription	Adipose Nuclei	Adipose
7	chr20:15955600-15957600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:15955800-15957400	Weak transcription	Primary B cells from cord blood	blood
9	chr20:15956000-15957800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr20:15956400-15956800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr20:15956400-15957800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr20:15956600-15957000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr20:15956600-15957200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr20:15956600-15957400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:15956600-15958800	Enhancers	HUES6 Cell Line	embryonic stem cell

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