Variant report

Variant	rs9294120
Chromosome Location	chr6:79308809-79308810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:79307983..79310728-chr6:79313328..79314875,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11751885	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11753657	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11755342	0.97[EUR][1000 genomes]
rs11756326	0.99[EUR][1000 genomes]
rs11757555	0.83[EUR][1000 genomes]
rs11759337	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16890184	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17332393	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55644721	0.96[EUR][1000 genomes]
rs55858016	0.88[EUR][1000 genomes]
rs55883909	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62426508	0.88[EUR][1000 genomes]
rs62426531	0.81[EUR][1000 genomes]
rs62426535	0.81[EUR][1000 genomes]
rs62426551	0.87[EUR][1000 genomes]
rs62426552	0.99[EUR][1000 genomes]
rs62426553	0.92[EUR][1000 genomes]
rs62426554	0.86[EUR][1000 genomes]
rs9443600	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9443601	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9443602	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9448490	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9448492	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9448495	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9448498	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9448499	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9448500	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9448505	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9448508	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886235	chr6:78861808-79369972	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv604011	chr6:79042990-79455282	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv886300	chr6:79129963-79341891	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv522646	chr6:79185106-79333988	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1028767	chr6:79200713-79341224	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9294120	CCDC47	trans	brain	seeQTL
rs9294120	LXN	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79307400-79309800	Enhancers	NH-A	brain
2	chr6:79307400-79310000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:79307400-79310000	Enhancers	HMEC	breast
4	chr6:79307400-79310000	Enhancers	NHLF	lung
5	chr6:79307400-79310600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:79307400-79310800	Enhancers	NHEK	skin
7	chr6:79307600-79310800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:79307600-79311200	Enhancers	HUVEC	blood vessel
9	chr6:79307800-79309000	Enhancers	Ovary	ovary
10	chr6:79307800-79309800	Enhancers	A549	lung
11	chr6:79307800-79310000	Enhancers	Hela-S3	cervix
12	chr6:79308000-79309400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr6:79308000-79309800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:79308000-79309800	Enhancers	Osteobl	bone
15	chr6:79308200-79309000	Enhancers	HSMMtube	muscle
16	chr6:79308200-79309200	Enhancers	Aorta	Aorta
17	chr6:79308200-79309600	Enhancers	HSMM	muscle
18	chr6:79308200-79309800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:79308200-79310200	Enhancers	NHDF-Ad	bronchial
20	chr6:79308400-79309400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:79308400-79309400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:79308400-79309400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:79308400-79309400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:79308400-79309400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:79308800-79309200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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