Variant report

Variant	rs9489521
Chromosome Location	chr6:119092219-119092220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119086471..119089736-chr6:119091626..119095598,3	K562	blood:
2	chr6:119091223..119093581-chr6:119115948..119118630,2	MCF-7	breast:
3	chr6:119090089..119093226-chr6:119095000..119099014,4	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10485389	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11963765	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17080604	0.90[ASN][1000 genomes]
rs17080617	0.83[ASN][1000 genomes]
rs2185560	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs284919	0.83[CHB][hapmap]
rs62424023	0.97[ASN][1000 genomes]
rs62424024	0.92[ASN][1000 genomes]
rs6909006	0.95[ASN][1000 genomes]
rs6910327	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs6910850	0.94[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7740511	0.95[ASN][1000 genomes]
rs7741194	0.87[ASN][1000 genomes]
rs7742473	0.87[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.87[ASN][1000 genomes]
rs7742814	0.94[ASN][1000 genomes]
rs7745728	0.98[ASN][1000 genomes]
rs7750777	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7758986	0.87[ASN][1000 genomes]
rs7765824	0.95[ASN][1000 genomes]
rs9320667	0.98[ASN][1000 genomes]
rs9489522	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9489523	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9489526	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs9489527	0.90[ASN][1000 genomes]
rs962393	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs9784804	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
12	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
13	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9489521	MCM9	cis	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119076800-119098000	Weak transcription	Psoas Muscle	Psoas
2	chr6:119078000-119093200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:119090400-119093000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:119090400-119093800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:119090400-119093800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:119090400-119094800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:119090400-119094800	Weak transcription	Placenta	Placenta
8	chr6:119090600-119093600	Weak transcription	HMEC	breast
9	chr6:119090600-119097400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:119090600-119097400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:119090600-119097600	Weak transcription	Primary T cells from cord blood	blood
12	chr6:119090600-119098000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:119090800-119092800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr6:119091000-119098000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:119091200-119092400	Enhancers	Fetal Thymus	thymus
16	chr6:119091400-119092600	Enhancers	Liver	Liver
17	chr6:119091600-119097600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:119092000-119092400	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr6:119092000-119092400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr6:119092000-119092600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:119092000-119095200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:119092200-119092400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:119092200-119096200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:119092200-119097600	Weak transcription	Osteobl	bone
25	chr6:119092200-119098000	Weak transcription	Stomach Mucosa	stomach

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