Variant report

Variant	rs6074709
Chromosome Location	chr20:1475635-1475636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:1475516-1475697	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SIRPB2	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1543423	0.81[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1884387	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2143832	0.88[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2873565	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795134	0.80[JPT][hapmap]
rs6033860	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs6033867	0.87[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6033901	0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6033910	0.99[ASN][1000 genomes]
rs6033950	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6042462	0.86[JPT][hapmap]
rs6042499	0.90[ASN][1000 genomes]
rs6042500	0.91[ASN][1000 genomes]
rs6042544	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6042592	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6042602	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6042611	0.97[ASN][1000 genomes]
rs6042650	0.94[ASN][1000 genomes]
rs6074715	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6074718	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6079277	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079288	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079289	0.92[ASN][1000 genomes]
rs6079294	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6079302	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6079317	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6079325	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs6079330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6079354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079376	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105233	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6105234	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105240	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6110169	0.93[ASN][1000 genomes]
rs6110207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110215	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110228	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110253	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6110261	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6110262	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6131543	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6131553	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6131559	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6135033	0.80[JPT][hapmap]
rs6135048	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6135050	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6135060	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6135061	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6135062	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6135063	0.93[ASN][1000 genomes]
rs6135064	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6135068	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135069	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135080	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6135089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6135105	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7270432	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs963867	0.88[CHB][hapmap];0.95[JPT][hapmap];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6074709	SIRPB2	cis	lung	GTEx
rs6074709	SIRPB2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1471600-1475800	Enhancers	Primary B cells from peripheral blood	blood
2	chr20:1471600-1478400	Weak transcription	NHEK	skin
3	chr20:1471600-1478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr20:1472200-1476000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr20:1472400-1476000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr20:1472600-1476200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr20:1473000-1476000	Enhancers	Primary B cells from cord blood	blood
8	chr20:1473000-1476000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:1473000-1479000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:1474000-1479800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr20:1475400-1480800	Weak transcription	Fetal Thymus	thymus
12	chr20:1475600-1476600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr20:1475600-1480800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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