Variant report

Variant	rs6079325
Chromosome Location	chr20:1467917-1467918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1543423	0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs1884387	0.94[ASN][1000 genomes]
rs2143832	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2873565	0.93[ASN][1000 genomes]
rs3795134	0.80[JPT][hapmap]
rs6033860	0.88[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs6033867	0.93[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs6033901	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6033910	0.94[ASN][1000 genomes]
rs6033950	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6033951	0.82[CHB][hapmap]
rs6042462	0.81[JPT][hapmap]
rs6042499	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6042500	0.95[ASN][1000 genomes]
rs6042544	0.88[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6042592	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6042602	1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6042611	0.91[ASN][1000 genomes]
rs6042650	0.89[ASN][1000 genomes]
rs6042667	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs6042675	0.82[CHB][hapmap]
rs6074709	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6074715	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6074718	0.84[ASN][1000 genomes]
rs6079277	0.93[ASN][1000 genomes]
rs6079288	0.94[ASN][1000 genomes]
rs6079289	0.96[ASN][1000 genomes]
rs6079294	0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6079302	0.94[ASN][1000 genomes]
rs6079317	0.89[ASN][1000 genomes]
rs6079330	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6079336	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs6079354	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6079361	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6079362	0.93[ASN][1000 genomes]
rs6079376	0.92[ASN][1000 genomes]
rs6105233	0.92[ASN][1000 genomes]
rs6105234	0.93[ASN][1000 genomes]
rs6105240	0.84[ASN][1000 genomes]
rs6110169	0.96[ASN][1000 genomes]
rs6110207	0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6110215	0.93[ASN][1000 genomes]
rs6110226	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6110228	0.89[ASN][1000 genomes]
rs6110253	0.84[ASN][1000 genomes]
rs6110261	0.82[ASN][1000 genomes]
rs6110262	0.81[ASN][1000 genomes]
rs6131543	0.93[ASN][1000 genomes]
rs6131553	0.96[ASN][1000 genomes]
rs6131559	0.92[ASN][1000 genomes]
rs6135033	0.80[JPT][hapmap]
rs6135048	0.93[ASN][1000 genomes]
rs6135050	0.93[ASN][1000 genomes]
rs6135060	0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs6135061	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6135062	0.95[ASN][1000 genomes]
rs6135063	0.93[ASN][1000 genomes]
rs6135064	0.94[ASN][1000 genomes]
rs6135068	0.97[ASN][1000 genomes]
rs6135069	0.97[ASN][1000 genomes]
rs6135080	0.97[ASN][1000 genomes]
rs6135089	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6135095	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6135105	0.93[ASN][1000 genomes]
rs7270432	0.84[ASN][1000 genomes]
rs963867	0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6079325	SIRPB2	cis	lung	GTEx
rs6079325	NSFL1C	cis	multi-tissue	Pritchard
rs6079325	TCF15	cis	cerebellum	SCAN
rs6079325	RP4-776F14.3	cis	Whole Blood	GTEx
rs6079325	SIRPB2	cis	Whole Blood	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1460800-1470200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr20:1462200-1469600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr20:1463600-1468200	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr20:1465600-1470000	Weak transcription	HUVEC	blood vessel
5	chr20:1466000-1468600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr20:1466000-1469400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr20:1466000-1470000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr20:1466000-1470000	Weak transcription	Hela-S3	cervix
9	chr20:1466200-1469000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr20:1466200-1469200	Weak transcription	HMEC	breast
11	chr20:1466800-1468800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr20:1467200-1469200	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
13	chr20:1467600-1469200	Weak transcription	NHEK	skin

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