Variant report

Variant	rs9463405
Chromosome Location	chr6:48394045-48394046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1013401	0.88[EUR][1000 genomes]
rs10456584	0.82[EUR][1000 genomes]
rs12202558	0.84[EUR][1000 genomes]
rs12664774	0.90[EUR][1000 genomes]
rs1348411	0.90[EUR][1000 genomes]
rs1373189	0.80[EUR][1000 genomes]
rs1373191	0.80[EUR][1000 genomes]
rs1582092	0.87[EUR][1000 genomes]
rs1582093	0.87[EUR][1000 genomes]
rs17289609	0.84[EUR][1000 genomes]
rs2078415	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2396863	0.90[EUR][1000 genomes]
rs2396865	0.90[EUR][1000 genomes]
rs2586826	0.85[EUR][1000 genomes]
rs2586827	0.87[EUR][1000 genomes]
rs2798765	0.80[EUR][1000 genomes]
rs2996265	0.84[EUR][1000 genomes]
rs2996266	0.84[EUR][1000 genomes]
rs2996267	0.83[EUR][1000 genomes]
rs34367220	0.90[EUR][1000 genomes]
rs6927980	0.94[EUR][1000 genomes]
rs9473361	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473384	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv603035	chr6:47902243-48700995	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1033151	chr6:48067287-48797029	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538217	chr6:48067287-48797029	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv885877	chr6:48117685-48626930	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv917050	chr6:48168742-48578496	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv830657	chr6:48387714-48566656	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9463405	RORC	trans	cerebellum	SCAN
rs9463405	SSFA2	trans	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:48390600-48394400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:48391400-48394200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr6:48392200-48394400	Weak transcription	Osteobl	bone
4	chr6:48392200-48396800	Weak transcription	NH-A	brain
5	chr6:48392800-48394200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:48393200-48394800	Enhancers	HUVEC	blood vessel
7	chr6:48393200-48395600	Enhancers	HMEC	breast
8	chr6:48393200-48398800	Enhancers	NHLF	lung
9	chr6:48393800-48395200	Enhancers	HSMM	muscle
10	chr6:48393800-48395400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:48393800-48398800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:48393800-48399000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:48394000-48394800	Weak transcription	NHDF-Ad	bronchial
14	chr6:48394000-48394800	Enhancers	NHEK	skin
15	chr6:48394000-48395600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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