Variant report

Variant	rs9489520
Chromosome Location	chr6:119080379-119080380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1022707	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1022708	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs11153782	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs1885125	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs2145569	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs4946372	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs4946373	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs4946382	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs6904381	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs6918844	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6934262	0.86[EUR][1000 genomes]
rs6939937	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs7381535	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7743045	0.80[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7754916	0.81[ASN][1000 genomes]
rs902780	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9320671	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs9374747	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9387621	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs9401106	0.84[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv464030	chr6:119043898-119080379	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv470855	chr6:119043898-119080379	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv604560	chr6:119043898-119080379	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv886568	chr6:119044453-119132164	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv886569	chr6:119055873-119132164	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv3333814	chr6:119078525-119100108	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9489520	ASF1A	Cis_1M	lymphoblastoid	RTeQTL
rs9489520	C6orf204	cis	cerebellum	SCAN
rs9489520	ASF1A	cis	cerebellum	SCAN
rs9489520	MCM9	cis	Liver	GTEx
rs9489520	C6orf61	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119076800-119098000	Weak transcription	Psoas Muscle	Psoas
2	chr6:119078000-119081800	Weak transcription	Stomach Mucosa	stomach
3	chr6:119078000-119093200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:119079200-119080600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr6:119079400-119081000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:119080000-119080400	Enhancers	Primary T cells from cord blood	blood
7	chr6:119080200-119082600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:119080200-119082600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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