Variant report

Variant	rs7862040
Chromosome Location	chr9:21465478-21465479
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21464451..21467378-chr9:21800569..21802345,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10491570	1.00[EUR][1000 genomes]
rs11998859	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11998894	0.97[LWK][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11999009	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12002122	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12004639	1.00[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16938422	0.82[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60371901	0.85[AFR][1000 genomes]
rs7021202	0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048384	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs7048663	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73649601	1.00[EUR][1000 genomes]
rs73652404	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73652406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7851158	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7856449	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7856562	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7858694	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	esv2752289	chr9:21361957-21499624	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv466297	chr9:21391698-21507589	Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613758	chr9:21391698-21507589	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv892739	chr9:21407250-21470520	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1030064	chr9:21455760-21524674	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	111 gene(s)	inside rSNPs	diseases
7	nsv613759	chr9:21455814-21492506	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1020445	chr9:21464962-21524162	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	109 gene(s)	inside rSNPs	diseases
9	nsv1020232	chr9:21464962-21524999	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	110 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21454800-21474400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:21454800-21481600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:21455200-21481000	Weak transcription	NHDF-Ad	bronchial
4	chr9:21455800-21481000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr9:21456000-21476600	Weak transcription	NHLF	lung
6	chr9:21461400-21466200	Strong transcription	NH-A	brain
7	chr9:21462000-21466000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:21462400-21466000	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr9:21462600-21466000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr9:21462600-21466800	Strong transcription	Osteobl	bone
11	chr9:21462600-21474600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:21463000-21502200	Weak transcription	HSMM	muscle
13	chr9:21463200-21465800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr9:21463200-21466000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:21464800-21466000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:21465000-21465800	Strong transcription	NHEK	skin
17	chr9:21465200-21465800	Strong transcription	A549	lung
18	chr9:21465200-21466000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:21465200-21468600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:21465400-21465800	Strong transcription	HMEC	breast
21	chr9:21465400-21474600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links